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

Project Information

SynBio4Flav

Grant agreement ID: 814650

DOI 10.3030/814650

Project closed

EC signature date 12 December 2018

Start date 1 January 2019

End date 31 August 2023

Funded under

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

Total cost € 7 371 051,25

EU contribution € 7 371 051,25

Coordinated by

AGENCIA ESTATAL CONSEJO SUPERIOR DE INVESTIGACIONES CIENTIFICAS
Spain

Deliverables

Documents, reports (8)

Project brochure and summary video

A printed project brochure summarizing the project and a video, which explains the project, displays the partners and describes the overall impact, will be produced.

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.

Press Release 2

A press release will inform about the project progress at M 36 - at the accumulation of major milestones. It will be translated into the languages of all consortium members to be distributed to the national press agencies and general media.

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.

Analysis of synthetic sequences released
Benefits and Risks assessment

Related with Tasks 5.4.1-4 involving DIFE, BIO and UNIOVI results

Press Release 3

A press release will announce the conclusion of the project highlighting the most important outcomes. It will be translated into the languages of all consortium members to be distributed to the national press agencies and general media

Publications

Peer reviewed articles (78)

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, Issue 10/14, 2020, ISSN 2331-8325
Publisher: Bio-Protocol
DOI: 10.21769/bioprotoc.3688

Propagation of Recombinant Genes through Complex Microbiomes with Synthetic Mini-RP4 Plasmid Vectors

Author(s): Aparicio, T., Silbert, J., Cepeda, S. and de Lorenzo, V.
Published in: BioDesign Research, Issue 26931257, 2022, ISSN 2693-1257
Publisher: American Association for the Advancement of Science
DOI: 10.34133/2022/9850305

Pressure‐dependent growth controls <scp>3D</scp> architecture of <i>Pseudomonas putida</i> microcolonies

Author(s): Juhyun Kim; Víctor de Lorenzo; Ángel Goñi‐Moreno
Published in: Environmental Microbiology Reports, Issue 41, 2023, ISSN 1758-2229
Publisher: Wiley-Blackwell
DOI: 10.1111/1758-2229.13182

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, Issue 10/8, 2021, Page(s) 1264, ISSN 2076-3921
Publisher: MDPI
DOI: 10.3390/antiox10081264

CRISPR/Cas9-enhanced Targetron Insertion for Delivery of Heterologous Sequences into the Genome of Gram-Negative Bacteria

Author(s): Velazquez, E., Al-Ramahi, Y. and de Lorenzo, V.
Published in: Current Protocols, Issue 26911299, 2022, ISSN 2691-1299
Publisher: John Wiley & Sons
DOI: 10.1002/cpz1.532

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, Issue 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

ssDNA recombineering boosts in vivo evolution of nanobodies displayed on bacterial surfaces

Author(s): Al-ramahi, Y., Nyerges, A., Margolles, Y., Cerdán, L., Ferenc G., Pál, C., Fernández, L.A. and de Lorenzo, V.
Published in: Communications Biology, Issue 23993642, 2021, ISSN 2399-3642
Publisher: Springer Nature
DOI: 10.1038/s42003-021-02702-0

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, Issue 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, Issue 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, Issue 21/22, 2020, Page(s) 3255-3265, ISSN 1439-4227
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/cbic.202000330

Deep learning-based kcat prediction enables improved enzyme-constrained model reconstruction

Author(s): Li F, Yuan L, Lu H, Li G, Chen Y, Engqvist MKM, Kerkhoven EJ, Nielsen J
Published in: Nature Catalysis, 2022, ISSN 2520-1158
Publisher: Springer Nature
DOI: 10.1038/s41929-022-00798-z

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, Issue 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, Issue 9/9, 2020, Page(s) 2477-2492, ISSN 2161-5063
Publisher: American Chemical Society
DOI: 10.1021/acssynbio.0c00272

Toward merging bottom-up and top-down model-based designing of synthetic microbial communities

Author(s): San León, D., Nogales, J.
Published in: Current Opinion in Microbiology, Issue 13695274, 2022, ISSN 1369-5274
Publisher: Elsevier BV
DOI: 10.1016/j.mib.2022.102169

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, Issue 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, Issue 23, 2021, ISSN 1462-2920
Publisher: John Wiley & Sons
DOI: 10.1111/1462-2920.15472

SEVA 4.0: an update of the Standard European Vector Architecture database for advanced analysis and programming of bacterial phenotypes. Nucleic Acids Res 51(D1):D1558-D1567. doi: 10.1093/nar/gkac1059.

Author(s): Martinez-Garcia E., Sofia F., Algar E., Aparicio T., Velázquez E.; Calles B., Tas, H., Blas, B., ; Martin B., Bruno; Prieto C., Sánchez-Sampedro L., Nørholm M., Daniel V., Wirth N., Dvorak P., Alejaldre L., Grozinger L., Crowther M., Goñi-Moreno A., Nikel, P.I., Nogales J., de Lorenzo V.
Published in: Nucleic Acids Research, 2023, ISSN 1362-4962
Publisher: Oxford University Press
DOI: 10.1093/nar/gkac1059

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, Issue 23/8, 2021, Page(s) 4418-4433, ISSN 1462-2912
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/1462-2920.15628

Targetron-assisted delivery of exogenous DNA sequences into Pseudomonas putida through CRISPR-aided counterselection

Author(s): Velázquez, V., Al-Ramahi, Y., Tellechea-Luzardo, J., Krasnogor, N., de Lorenzo, V.
Published in: ACS Synthetic Biology, Issue 21615063, 2021, ISSN 2161-5063
Publisher: American Chemical Society
DOI: 10.1021/acssynbio.1c00199

<i>In Vivo</i> Sampling of Intracellular Heterogeneity of <i>Pseudomonas putida</i> Enables Multiobjective Optimization of Genetic Devices

Author(s): Angeles Hueso-Gil; Belén Calles; Víctor de Lorenzo
Published in: ACS Synthetic Biology, Issue 40, 2023, ISSN 2161-5063
Publisher: American Chemical Society
DOI: 10.1021/acssynbio.3c00009

Evaluation of double expression system for co-expression and co-immobilization of flavonoid glucosylation cascade

Author(s): Agata Matera, Kinga Dulak, Sandra Sordon, Kacper Waśniewski, Ewa Huszcza, Jarosław Popłoński
Published in: Applied Microbiology and Biotechnology, 2022, ISSN 1432-0614
Publisher: Springer Nature
DOI: 10.1007/s00253-022-12259-5

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

Flavonoid-Modifying Capabilities of the Human Gut Microbiome—An In Silico Study

Author(s): Tobias Goris, Rafael RC Cuadrat, Annett Braune
Published in: Nutrients, Issue 20726643, 2021, ISSN 2072-6643
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/nu13082688

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, Issue 1, 2021, ISSN 2397-7000
Publisher: Oxford University Press
DOI: 10.1093/synbio/ysab024

Water potential governs effector specificity of the transcriptional regulator XylR of Pseudomonas putida

Author(s): Dvořák, P., Calcagno Galvão, T., Pflüger-Grau, K., Banks, A.M., de Lorenzo, V. and Jiménez, J.I.
Published in: Environmental Microbiology, 2023, ISSN 1462-2920
Publisher: John Wiley & Sons
DOI: 10.1111/1462-2920.16342

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, Issue 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, Issue 11/1, 2020, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-020-20230-z

Synthetic Biology─High Time to Deliver?

Author(s): Andrew D. Hanson; Víctor de Lorenzo
Published in: ACS Synthetic Biology, Issue 38, 2023, ISSN 2161-5063
Publisher: American Chemical Society
DOI: 10.1021/acssynbio.3c00238

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, Issue 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

Optimized De Novo Eriodictyol Biosynthesis in Streptomyces albidoflavus Using an Expansion of the Golden Standard Toolkit for Its Use in Actinomycetes

Author(s): Magadán-Corpas, P., Ye, S., Pérez-Valero, A., MacAlpine, P. L., Valdés-Chiara, P., Torres-Bacete, J., Nogales, J., Villar, C. J., Lombó, F.
Published in: International Journal of Molecular Sciences, 2023, ISSN 1422-0067
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms24108879

The four Fs of the knowledge-based BioEconomy – A homage to Christian Patermann

Author(s): de Lorenzo, V.
Published in: EFB Bioeconomy Journal, Issue 26670410, 2022, ISSN 2667-0410
Publisher: Elsevier
DOI: 10.1016/j.bioeco.2022.100035

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, Issue 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, Issue 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, Issue 24, 2021, ISSN 1618-1905
Publisher: Springer-Nature
DOI: 10.1007/s10123-021-00194-w

Versioning biological cells for trustworthy cell engineering

Author(s): Tellechea-Luzardo, J., Hobbs, L., Velázquez, E., Pelechova E., Woods, S., de Lorenzo, V. and Krasnogor, N.
Published in: Nature Communications, Issue 20411723, 2022, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-022-28350-4

Environmental Galenics: large-scale fortification of extant microbiomes with engineered bioremediation agents.

Author(s): de Lorenzo, V.
Published in: Philosophical transactions of the Royal Society B, Issue 09628436, 2022, ISSN 0962-8436
Publisher: Royal Society of London
DOI: 10.1098/rstb.2021.0395

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, Issue 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

Hypermutation of specific genomic loci of Pseudomonas putida for continuous evolution of target genes

Author(s): Velázquez, E., Álvarez, B., Fernández, L.A. and de Lorenzo, V.
Published in: Microbial Biotechnology, Issue 17517915, 2022, ISSN 1751-7915
Publisher: John Wiley & Sons
DOI: 10.1111/1751-7915.14098

Innovation vs. novelty in microbial systems

Author(s): de Lorenzo, V.
Published in: Environmental Microbioly, 2023, ISSN 1462-2920
Publisher: John Wiley & Sons
DOI: 10.1111/1462-2920.16278

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, Issue 143, 2021, Page(s) 112241, ISSN 0753-3322
Publisher: Elsevier Masson
DOI: 10.1016/j.biopha.2021.112241

Advances in constraint-based models: methods for improved predictive power based on resource allocation constraints.

Author(s): Kerkhoven, EJ
Published in: Current Opinion in Microbiology, Issue 13695274, 2022, ISSN 1369-5274
Publisher: Elsevier BV
DOI: 10.1016/j.mib.2022.102168

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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 54, 2019, Page(s) 200-211, ISSN 1096-7176
Publisher: Academic Press
DOI: 10.1016/j.ymben.2019.04.005

A <i>p</i>-Coumaroyl-CoA Biosensor for Dynamic Regulation of Naringenin Biosynthesis in <i>Saccharomyces cerevisiae</i>

Author(s): Dany Liu; Maria Sole Sica; Jiwei Mao; Lucy Fang-I Chao; Verena Siewers
Published in: ACS Synthetic Biology vol.In Press(2022), Issue 2, 2022, ISSN 2161-5063
Publisher: American Chemical Society
DOI: 10.1021/acssynbio.2c00111

Novel flavonoid C-8 hydroxylase from Rhodotorula glutinis: identification, characterization and substrate scope

Author(s): Dulak Kinga, Sordon Sandra, Matera Agata, Bartosz Kozak, Ewa Huszcza, Jarosław Popłoński
Published in: Microbial Cell Factories, 2022, ISSN 1475-2859
Publisher: BioMed Central
DOI: 10.1186/s12934-022-01899-x

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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 4, 2021, ISSN 2397-7000
Publisher: Oxfor University Press
DOI: 10.1093/synbio/ysab030

Discovery of Novel Tyrosine Ammonia Lyases for the Enzymatic Synthesis of p-Coumaric Acid

Author(s): Yannik Brack, Chenghai Sun, Dong Yi, Uwe T. Bornscheuer
Published in: ChemBioChem, Issue 14394227, 2022, ISSN 1439-4227
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/cbic.202200062

Technical upgrade of an open-source liquid handler to support bacterial colony screening

Author(s): del Olmo Lianes, I., Yubero, P., Gómez-Luengo, A., Nogales, J., Espeso, D.
Published in: Frontiers in Bioengineering and Biotechnology, 2023, ISSN 2296-4185
Publisher: Frontiers Media S.A.
DOI: 10.3389/fbioe.2023.1202836

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

System metabolic engineering of Escherichia coli W for the production of 2-ketoisovalerate using unconventional feedstock

Author(s): Darwin Carranza-Saavedra; Jesús Torres-Bacete; Blas Blázquez; Claudia Patricia Sánchez Henao; José Edgar Zapata Montoya; Juan Nogales
Published in: Frontiers in Bioengineering and Biotechnology, Issue 32, 2023, ISSN 2296-4185
Publisher: Frontiers Media S.A.
DOI: 10.3389/fbioe.2023.1176445

Missing Links Between Gene Function and Physiology in Genomics

Author(s): Collado-Vides, J., Gaudet, P and de Lorenzo, V.
Published in: Frontiers in Physiology, Issue 1664042X, 2022, ISSN 1664-042X
Publisher: Frontiers Research Foundation
DOI: 10.3389/fphys.2022.815874

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

Optimizing yeast for high-level production of kaempferol and quercetin

Author(s): Musa Tartik, Juan Liu, Marta Tous Mohedano, Jiwei Mao, Yun Chen
Published in: Microbial Cell Factories, 2023, ISSN 1475-2859
Publisher: BioMed Central
DOI: 10.1186/s12934-023-02084-4

Golden Standard: a complete standard, portable, and interoperative MoClo tool for model and non-model proteobacteria.

Author(s): Blázquez, B., San León, D., Torres-Bacete, J., Gómez-Luengo, Á., Kniewel, R., Martínez, I., Sordon, S., Wilczak, A., Salgado, S. Huszcza, E., Popłoński, J., Prieto, A., Nogales, J.
Published in: Nucleic Acids Research, 2023, ISSN 1362-4962
Publisher: Oxford University Press
DOI: 10.1093/nar/gkad758

Standardization of regulatory nodes for engineering heterologous gene expression: a feasibility study

Author(s): Nikel, P.I., Benedetti, I., Wirth, N.T., de Lorenzo, V. and Calles, B.
Published in: Microbial Biotechnology, Issue 17517915, 2022, ISSN 1751-7915
Publisher: John Wiley and Sons
DOI: 10.1111/1751-7915.14063

Other (4)

Transformation of flavonoids by human gut microbiota – from in silico analyses to experimental confirmation

Author(s): Tobias Goris, Annett Braune
Published in: Abstract Book - International Conference on Polyphenols, 2022
Publisher: ICPH Conference

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

Conference proceedings (4)

Insights on Metabolic Features of Bacillus subtilis Based on Multistrain Genome-Scale Metabolic Modeling

Author(s): San León Granado, David; Blázquez, Blas; Nogales, Juan
Published in: International Journal of Molecular Sciences, Issue 37, 2023, ISSN 1422-0067
Publisher: MDPI
DOI: 10.5281/zenodo.8171332

Modular synthetic biology toolkit in Streptomyces for flavonoids biosynthesis and cellular chassis engineering

Author(s): Suhui Ye, Patricia Magadán-Corpas, Álvaro Pérez-Valero, Jesús Torres-Bacete, Juan Nogales, Claudio J. Villar, Felipe Lombó
Published in: 2022
Publisher: 3rd Synthetic Biology of Natural Products Conference

De novo biosynthesis of o-methylated flavonoids in the microbial factory Streptomyces albus

Author(s): Álvaro Pérez-Valero, Suhui Ye, Patricia Magadán-Corpas, Claudio J. Villar, Felipe Lombó
Published in: 2022
Publisher: 3rd Synthetic Biology of Natural Products Conference

Improvement in flavonoids production combining different strategies

Author(s): Patricia Magadán-Corpas, Suhui Ye, Álvaro Pérez-Valero, Claudio J. Villar, Felipe Lombó
Published in: 2022
Publisher: 3rd Synthetic Biology of Natural Products Conference

Book chapters (2)

Living architecture: metabolic applications for next-generation, selectively programmable bioreactors

Author(s): Molly Hogle, Barbara Imhof, Waltraut Hoheneder, Rachel Armstrong, Ioannis Ieropoulos, Lauren Wallis, Jiseon You, Juan Nogales. Ed. Peter Droege
Published in: Urban and Regional Agriculture. Building Resilient Food Systems, 2023, ISBN 9780128202869
Publisher: Elsevier
DOI: 10.1016/b978-0-12-820286-9.00004-2

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

Monographic books (1)

High-Efficiency Multi-site Genomic Editing (HEMSE) Made Easy

Author(s): Aparicio, T., de Lorenzo, V., Martínez-García, E.
Published in: Methods in Molecular Biology, 2022, ISBN 978-1-0716-2232-2
Publisher: Humana
DOI: 10.1007/978-1-0716-2233-9_4

Non-peer reviewed articles (1)

Golden Standard: A complete standard, portable, and interoperative MoClo tool for model and non-model bacterial hosts

Author(s): Blas Blázquez, Jesús Torres-Bacete, David San Leon, Ryan Kniewel, Igor Martinez, Sandra Sordon, Aleksandra Wilczak, Sergio Salgado, Ewa Huszcza, Jarosław Popłoński, M. Auxiliadora Prieto, Juan Nogales
Published in: bioRxiv, Issue 26928205, 2022, ISSN 2692-8205
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2022.09.20.508659