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

Rezultaty

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

Publikacje

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

Autorzy: Gonzalo Durante-Rodríguez, Belén Calles, Víctor Lorenzo, Pablo Nikel
Opublikowane w: BIO-PROTOCOL, Numer 10/14, 2020, ISSN 2331-8325
Wydawca: Bio-Protocol
DOI: 10.21769/bioprotoc.3688

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

Autorzy: Aparicio, T., Silbert, J., Cepeda, S. and de Lorenzo, V.
Opublikowane w: BioDesign Research, Numer 26931257, 2022, ISSN 2693-1257
Wydawca: American Association for the Advancement of Science
DOI: 10.34133/2022/9850305

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

Autorzy: Juhyun Kim; Víctor de Lorenzo; Ángel Goñi‐Moreno
Opublikowane w: Environmental Microbiology Reports, Numer 41, 2023, ISSN 1758-2229
Wydawca: Wiley-Blackwell
DOI: 10.1111/1758-2229.13182

Quantitative assessment of morphological traits of planktonic bacterial aggregates

Autorzy: Espeso, D.R., Martínez-García, E., de Lorenzo, V.
Opublikowane w: Water Research, 2020, ISSN 0043-1354
Wydawca: Elsevier BV
DOI: 10.1016/j.watres.2020.116468

Terpenoids and Polyphenols as Natural Antioxidant Agents in Food Preservation

Autorzy: 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
Opublikowane w: Antioxidants, Numer 10/8, 2021, Strona(/y) 1264, ISSN 2076-3921
Wydawca: MDPI
DOI: 10.3390/antiox10081264

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

Autorzy: Velazquez, E., Al-Ramahi, Y. and de Lorenzo, V.
Opublikowane w: Current Protocols, Numer 26911299, 2022, ISSN 2691-1299
Wydawca: 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

Autorzy: 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
Opublikowane w: Angewandte Chemie, Numer 133/31, 2021, Strona(/y) 17011-17016, ISSN 0044-8249
Wydawca: John Wiley & Sons Ltd.
DOI: 10.1002/ange.202107182

Recent advances in model-assisted metabolic engineering

Autorzy: Steinn Gudmundsson, Juan Nogales
Opublikowane w: Current Opinion in Systems Biology, 2021, Strona(/y) 100392, ISSN 2452-3100
Wydawca: Elsevier
DOI: 10.1016/j.coisb.2021.100392

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

Autorzy: Al-ramahi, Y., Nyerges, A., Margolles, Y., Cerdán, L., Ferenc G., Pál, C., Fernández, L.A. and de Lorenzo, V.
Opublikowane w: Communications Biology, Numer 23993642, 2021, ISSN 2399-3642
Wydawca: 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

Autorzy: Jesús Torres‐Bacete, José Luís García, Juan Nogales
Opublikowane w: Microbial Biotechnology, 2021, ISSN 1751-7915
Wydawca: 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

Autorzy: 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
Opublikowane w: Angewandte Chemie International Edition, Numer 60/31, 2021, Strona(/y) 16874-16879, ISSN 1433-7851
Wydawca: John Wiley & Sons Ltd.
DOI: 10.1002/anie.202107182

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

Autorzy: Espeso D. R., Algar, E., Martínez-García, E., de Lorenzo, V.
Opublikowane w: BMC Bioinformatics, 2020, ISSN 1471-2105
Wydawca: BioMed Central
DOI: 10.1186/s12859-020-3490-1

Contextual dependencies expand the re-usability of genetic inverters

Autorzy: Huseyin Tas, Lewis Grozinger, Ruud Stoof, Victor de Lorenzo, Ángel Goñi-Moreno
Opublikowane w: Nature Communications, Numer 12/1, 2021, ISSN 2041-1723
Wydawca: Nature Publishing Group
DOI: 10.1038/s41467-020-20656-5

Environmental Performance of Pseudomonas putida with a Uracylated Genome

Autorzy: Elena Algar, Yamal Al‐Ramahi, Víctor Lorenzo, Esteban Martínez‐García
Opublikowane w: ChemBioChem, Numer 21/22, 2020, Strona(/y) 3255-3265, ISSN 1439-4227
Wydawca: John Wiley & Sons Ltd.
DOI: 10.1002/cbic.202000330

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

Autorzy: Li F, Yuan L, Lu H, Li G, Chen Y, Engqvist MKM, Kerkhoven EJ, Nielsen J
Opublikowane w: Nature Catalysis, 2022, ISSN 2520-1158
Wydawca: 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

Autorzy: Huseyin Tas, Ángel Goñi-Moreno, Víctor de Lorenzo
Opublikowane w: ACS Synthetic Biology, Numer 10/1, 2021, Strona(/y) 213-217, ISSN 2161-5063
Wydawca: American Chemical Society
DOI: 10.1021/acssynbio.0c00529

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

Autorzy: Esteban Martínez-García, Sofía Fraile, David Rodríguez Espeso, Davide Vecchietti, Giovanni Bertoni, Víctor de Lorenzo
Opublikowane w: ACS Synthetic Biology, Numer 9/9, 2020, Strona(/y) 2477-2492, ISSN 2161-5063
Wydawca: American Chemical Society
DOI: 10.1021/acssynbio.0c00272

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

Autorzy: San León, D., Nogales, J.
Opublikowane w: Current Opinion in Microbiology, Numer 13695274, 2022, ISSN 1369-5274
Wydawca: Elsevier BV
DOI: 10.1016/j.mib.2022.102169

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

Autorzy: Sofía Fraile, María Briones, Mónica Revenga-Parra, Víctor de Lorenzo, Encarnación Lorenzo, Esteban Martínez-García
Opublikowane w: ACS Synthetic Biology, Numer 10/8, 2021, Strona(/y) 2049-2059, ISSN 2161-5063
Wydawca: 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

Autorzy: Danilo P´érez-Pantoja; Victor De Lorenzo; Pablo Ivan Nikel; Max Chavarría
Opublikowane w: Environmental Microbiology, Numer 23, 2021, ISSN 1462-2920
Wydawca: 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.

Autorzy: 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.
Opublikowane w: Nucleic Acids Research, 2023, ISSN 1362-4962
Wydawca: 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

Autorzy: Pavel Dvořák, Carlos Alvarez‐Carreño, Sergio Ciordia, Alberto Paradela, Víctor Lorenzo
Opublikowane w: Environmental Microbiology, Numer 23/8, 2021, Strona(/y) 4418-4433, ISSN 1462-2912
Wydawca: Blackwell Publishing Inc.
DOI: 10.1111/1462-2920.15628

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

Autorzy: Velázquez, V., Al-Ramahi, Y., Tellechea-Luzardo, J., Krasnogor, N., de Lorenzo, V.
Opublikowane w: ACS Synthetic Biology, Numer 21615063, 2021, ISSN 2161-5063
Wydawca: American Chemical Society
DOI: 10.1021/acssynbio.1c00199

In Vivo Sampling of Intracellular Heterogeneity of Pseudomonas putida Enables Multiobjective Optimization of Genetic Devices

Autorzy: Angeles Hueso-Gil; Belén Calles; Víctor de Lorenzo
Opublikowane w: ACS Synthetic Biology, Numer 40, 2023, ISSN 2161-5063
Wydawca: American Chemical Society
DOI: 10.1021/acssynbio.3c00009

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

Autorzy: Agata Matera, Kinga Dulak, Sandra Sordon, Kacper Waśniewski, Ewa Huszcza, Jarosław Popłoński
Opublikowane w: Applied Microbiology and Biotechnology, 2022, ISSN 1432-0614
Wydawca: Springer Nature
DOI: 10.1007/s00253-022-12259-5

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

Autorzy: Pablo I. Nikel, Tobias Fuhrer, Max Chavarría, Alberto Sánchez-Pascuala, Uwe Sauer, Víctor de Lorenzo
Opublikowane w: The ISME Journal, 2021, ISSN 1751-7362
Wydawca: Nature Publishing Group
DOI: 10.1038/s41396-020-00884-9

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

Autorzy: Tobias Goris, Rafael RC Cuadrat, Annett Braune
Opublikowane w: Nutrients, Numer 20726643, 2021, ISSN 2072-6643
Wydawca: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/nu13082688

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

Autorzy: Huseyin Tas; Lewis Grozinger; Angel Goñi-Moreno; Angel Goñi-Moreno; Víctor de Lorenzo
Opublikowane w: Synthetic Biology, Numer 1, 2021, ISSN 2397-7000
Wydawca: Oxford University Press
DOI: 10.1093/synbio/ysab024

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

Autorzy: Dvořák, P., Calcagno Galvão, T., Pflüger-Grau, K., Banks, A.M., de Lorenzo, V. and Jiménez, J.I.
Opublikowane w: Environmental Microbiology, 2023, ISSN 1462-2920
Wydawca: 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

Autorzy: Pavel Dvořák, Jozef Kováč, Víctor Lorenzo
Opublikowane w: Microbial Biotechnology, Numer 13/4, 2020, Strona(/y) 1273-1283, ISSN 1751-7915
Wydawca: 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

Autorzy: Beatriz Álvarez, Mario Mencía, Víctor de Lorenzo, Luis Ángel Fernández
Opublikowane w: Nature Communications, Numer 11/1, 2020, ISSN 2041-1723
Wydawca: Nature Publishing Group
DOI: 10.1038/s41467-020-20230-z

Synthetic Biology─High Time to Deliver?

Autorzy: Andrew D. Hanson; Víctor de Lorenzo
Opublikowane w: ACS Synthetic Biology, Numer 38, 2023, ISSN 2161-5063
Wydawca: American Chemical Society
DOI: 10.1021/acssynbio.3c00238

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

Autorzy: 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.
Opublikowane w: Cell Host & Microbe, 2020, ISSN 1934-6069
Wydawca: Elsevier
DOI: 10.1016/j.chom.2020.05.006

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

Autorzy: Quanli Liu, Tao Yu, Xiaowei Li, Yu Chen, Kate Campbell, Jens Nielsen, Yun Chen
Opublikowane w: Nature Communications, Numer 10/1, 2019, ISSN 2041-1723
Wydawca: 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

Autorzy: Laura Marín, Ignacio Gutiérrez‐del‐Río, Claudio Jesús Villar, Felipe Lombó
Opublikowane w: Microbial Biotechnology, 2021, ISSN 1751-7915
Wydawca: John Wiley & Sons
DOI: 10.1111/1751-7915.13874

An automated DIY framework for experimental evolution of Pseudomonas putida

Autorzy: David R. Espeso, Pavel Dvořák, Tomás Aparicio, Víctor Lorenzo
Opublikowane w: Microbial Biotechnology, 2020, ISSN 1751-7915
Wydawca: 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

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

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

Autorzy: de Lorenzo, V.
Opublikowane w: EFB Bioeconomy Journal, Numer 26670410, 2022, ISSN 2667-0410
Wydawca: Elsevier
DOI: 10.1016/j.bioeco.2022.100035

Recent trends in biocatalysis

Autorzy: Dong Yi, Thomas Bayer, Christoffel P. S. Badenhorst, Shuke Wu, Mark Doerr, Matthias Höhne, Uwe T. Bornscheuer
Opublikowane w: Chemical Society Reviews, Numer 50/14, 2021, Strona(/y) 8003-8049, ISSN 0306-0012
Wydawca: Royal Society of Chemistry
DOI: 10.1039/d0cs01575j

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

Autorzy: Pavel Dvořák, Edward A. Bayer, Víctor de Lorenzo
Opublikowane w: ACS Synthetic Biology, Numer 9/10, 2020, Strona(/y) 2749-2764, ISSN 2161-5063
Wydawca: American Chemical Society
DOI: 10.1021/acssynbio.0c00276

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

Autorzy: Juhyun Kim; Rafael Silva-Rocha; Víctor de Lorenzo
Opublikowane w: International Microbiology, Numer 24, 2021, ISSN 1618-1905
Wydawca: Springer-Nature
DOI: 10.1007/s10123-021-00194-w

Versioning biological cells for trustworthy cell engineering

Autorzy: Tellechea-Luzardo, J., Hobbs, L., Velázquez, E., Pelechova E., Woods, S., de Lorenzo, V. and Krasnogor, N.
Opublikowane w: Nature Communications, Numer 20411723, 2022, ISSN 2041-1723
Wydawca: Nature Publishing Group
DOI: 10.1038/s41467-022-28350-4

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

Autorzy: de Lorenzo, V.
Opublikowane w: Philosophical transactions of the Royal Society B, Numer 09628436, 2022, ISSN 0962-8436
Wydawca: 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

Autorzy: Cheewin Kittikunapong, Suhui Ye, Patricia Magadán-Corpas, Álvaro Pérez-Valero, Claudio J. Villar, Felipe Lombó, Eduard J. Kerkhoven
Opublikowane w: Metabolites, Numer 11/5, 2021, Strona(/y) 304, ISSN 2218-1989
Wydawca: MDPI
DOI: 10.3390/metabo11050304

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

Autorzy: Özlem Akkaya, Tomás Aparicio, Danilo Pérez‐Pantoja, Víctor Lorenzo
Opublikowane w: Environmental Microbiology, 2021, ISSN 1462-2912
Wydawca: Blackwell Publishing Inc.
DOI: 10.1111/1462-2920.15384

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

Autorzy: Velázquez, E., Álvarez, B., Fernández, L.A. and de Lorenzo, V.
Opublikowane w: Microbial Biotechnology, Numer 17517915, 2022, ISSN 1751-7915
Wydawca: John Wiley & Sons
DOI: 10.1111/1751-7915.14098

Innovation vs. novelty in microbial systems

Autorzy: de Lorenzo, V.
Opublikowane w: Environmental Microbioly, 2023, ISSN 1462-2920
Wydawca: John Wiley & Sons
DOI: 10.1111/1462-2920.16278

Antiproliferative and palliative activity of flavonoids in colorectal cancer

Autorzy: Javier Fernández, Blanca Silván, Rodrigo Entrialgo-Cadierno, Claudio J. Villar, Raffaele Capasso, José Antonio Uranga, Felipe Lombó, Raquel Abalo
Opublikowane w: Biomedicine & Pharmacotherapy, Numer 143, 2021, Strona(/y) 112241, ISSN 0753-3322
Wydawca: Elsevier Masson
DOI: 10.1016/j.biopha.2021.112241

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

Autorzy: Kerkhoven, EJ
Opublikowane w: Current Opinion in Microbiology, Numer 13695274, 2022, ISSN 1369-5274
Wydawca: Elsevier BV
DOI: 10.1016/j.mib.2022.102168

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

Autorzy: Juan Nogales, Joshua Mueller, Steinn Gudmundsson, Francisco J. Canalejo, Estrella Duque, Jonathan Monk, Adam M. Feist, Juan Luis Ramos, Wei Niu, Bernhard O. Palsson
Opublikowane w: Environmental Microbiology, Numer 22/1, 2019, Strona(/y) 255-269, ISSN 1462-2912
Wydawca: Blackwell Publishing Inc.
DOI: 10.1111/1462-2920.14843

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

Autorzy: Belén Calles, Ángel Goñi‐Moreno, Víctor Lorenzo
Opublikowane w: Molecular Systems Biology, Numer 15/12, 2019, ISSN 1744-4292
Wydawca: Nature Publishing Group
DOI: 10.15252/msb.20188777

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

Autorzy: Tomas Aparicio, Akos Nyerges, Esteban Martínez-García, Víctor de Lorenzo
Opublikowane w: iScience, Numer 23/3, 2020, Strona(/y) 100946, ISSN 2589-0042
Wydawca: Elsevier
DOI: 10.1016/j.isci.2020.100946

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

Autorzy: Angeles Hueso-Gil, Ákos Nyerges, Csaba Pál, Belén Calles, Víctor de Lorenzo
Opublikowane w: ACS Synthetic Biology, Numer 9/1, 2019, Strona(/y) 104-114, ISSN 2161-5063
Wydawca: American Chemical Society
DOI: 10.1021/acssynbio.9b00375

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

Autorzy: Elena Velázquez, Víctor de Lorenzo, Yamal Al-Ramahi
Opublikowane w: ACS Synthetic Biology, Numer 8/9, 2019, Strona(/y) 2186-2193, ISSN 2161-5063
Wydawca: 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

Autorzy: 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
Opublikowane w: Nucleic Acids Research, Numer 48/D1, 2019, Strona(/y) D1164-D1170, ISSN 0305-1048
Wydawca: Oxford University Press
DOI: 10.1093/nar/gkz1024

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

Autorzy: David Espeso, Esteban Martínez-García, Víctor Lorenzo
Opublikowane w: BIO-PROTOCOL, Numer 9/10, 2019, ISSN 2331-8325
Wydawca: Bio-protocol
DOI: 10.21769/bioprotoc.3238

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

Autorzy: Tomas Aparicio, Akos Nyerges, István Nagy, Csaba Pal, Esteban Martínez‐García, Víctor Lorenzo
Opublikowane w: Environmental Microbiology, Numer 22/1, 2019, Strona(/y) 45-58, ISSN 1462-2912
Wydawca: Blackwell Publishing Inc.
DOI: 10.1111/1462-2920.14814

Pseudomonas putida in the quest of programmable chemistry

Autorzy: Esteban Martínez-García, Víctor de Lorenzo
Opublikowane w: Current Opinion in Biotechnology, Numer 59, 2019, Strona(/y) 111-121, ISSN 0958-1669
Wydawca: Elsevier BV
DOI: 10.1016/j.copbio.2019.03.012

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

Autorzy: Alberto Sánchez-Pascuala, Lorena Fernández-Cabezón, Víctor de Lorenzo, Pablo I. Nikel
Opublikowane w: Metabolic Engineering, Numer 54, 2019, Strona(/y) 200-211, ISSN 1096-7176
Wydawca: Academic Press
DOI: 10.1016/j.ymben.2019.04.005

A p-Coumaroyl-CoA Biosensor for Dynamic Regulation of Naringenin Biosynthesis in Saccharomyces cerevisiae

Autorzy: Dany Liu; Maria Sole Sica; Jiwei Mao; Lucy Fang-I Chao; Verena Siewers
Opublikowane w: ACS Synthetic Biology vol.In Press(2022), Numer 2, 2022, ISSN 2161-5063
Wydawca: American Chemical Society
DOI: 10.1021/acssynbio.2c00111

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

Autorzy: Dulak Kinga, Sordon Sandra, Matera Agata, Bartosz Kozak, Ewa Huszcza, Jarosław Popłoński
Opublikowane w: Microbial Cell Factories, 2022, ISSN 1475-2859
Wydawca: BioMed Central
DOI: 10.1186/s12934-022-01899-x

Concomitant prediction of environmental fate and toxicity of chemical compounds

Autorzy: Juan Antonio Garcia-Martin, Max Chavarría, Victor de Lorenzo, Florencio Pazos
Opublikowane w: Biology Methods and Protocols, Numer 5/1, 2020, ISSN 2396-8923
Wydawca: Oxford University Press
DOI: 10.1093/biomethods/bpaa025

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

Autorzy: Ángeles Hueso‐Gil, Belén Calles, Víctor Lorenzo
Opublikowane w: Environmental Microbiology, Numer 22/8, 2020, Strona(/y) 3535-3547, ISSN 1462-2912
Wydawca: Blackwell Publishing Inc.
DOI: 10.1111/1462-2920.15126

Metabolic modelling approaches for describing and engineering microbial communities

Autorzy: Beatriz García-Jiménez, Jesús Torres-Bacete, Juan Nogales
Opublikowane w: Computational and Structural Biotechnology Journal, Numer 19, 2021, Strona(/y) 226-246, ISSN 2001-0370
Wydawca: Elsevier
DOI: 10.1016/j.csbj.2020.12.003

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

Autorzy: Víctor de Lorenzo, Natalio Krasnogor, Markus Schmidt
Opublikowane w: New Biotechnology, Numer 60, 2021, Strona(/y) 44-51, ISSN 1871-6784
Wydawca: 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

Autorzy: Juhyun Kim, Angel Goñi-Moreno, Víctor de Lorenzo
Opublikowane w: mBio, Numer 12/1, 2021, ISSN 2150-7511
Wydawca: American Society for Microbiology
DOI: 10.1128/mbio.03685-20

Multifunctional SEVA shuttle vectors for actinomycetes and Gram‐negative bacteria

Autorzy: Coral García‐Gutiérrez, Tomás Aparicio, Lucía Torres‐Sánchez, Esteban Martínez‐García, Víctor Lorenzo, Claudio J. Villar, Felipe Lombó
Opublikowane w: MicrobiologyOpen, Numer 9/6, 2020, Strona(/y) 1135-1149, ISSN 2045-8827
Wydawca: 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

Autorzy: Alejandro Arce‐Rodríguez, Pablo I. Nikel, Belén Calles, Max Chavarría, Raúl Platero, Tino Krell, Victor Lorenzo
Opublikowane w: Environmental Microbiology, 2021, ISSN 1462-2912
Wydawca: 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

Autorzy: Alejandro Arce-Rodríguez; Alejandro Arce-Rodríguez; Ilaria Benedetti; José Manuel Borrero-de Acuña; Rafael Silva-Rocha; Rafael Silva-Rocha; Víctor de Lorenzo
Opublikowane w: Synthetic Biology, Numer 4, 2021, ISSN 2397-7000
Wydawca: Oxfor University Press
DOI: 10.1093/synbio/ysab030

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

Autorzy: Yannik Brack, Chenghai Sun, Dong Yi, Uwe T. Bornscheuer
Opublikowane w: ChemBioChem, Numer 14394227, 2022, ISSN 1439-4227
Wydawca: John Wiley & Sons Ltd.
DOI: 10.1002/cbic.202200062

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

Autorzy: del Olmo Lianes, I., Yubero, P., Gómez-Luengo, A., Nogales, J., Espeso, D.
Opublikowane w: Frontiers in Bioengineering and Biotechnology, 2023, ISSN 2296-4185
Wydawca: Frontiers Media S.A.
DOI: 10.3389/fbioe.2023.1202836

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

Autorzy: Páez-Espino, A.D., Nikel, P., Chavarría, M., de Lorenzo, V.
Opublikowane w: Environmental Microbiology, 2020, ISSN 1462-2912
Wydawca: 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

Autorzy: Darwin Carranza-Saavedra; Jesús Torres-Bacete; Blas Blázquez; Claudia Patricia Sánchez Henao; José Edgar Zapata Montoya; Juan Nogales
Opublikowane w: Frontiers in Bioengineering and Biotechnology, Numer 32, 2023, ISSN 2296-4185
Wydawca: Frontiers Media S.A.
DOI: 10.3389/fbioe.2023.1176445

Missing Links Between Gene Function and Physiology in Genomics

Autorzy: Collado-Vides, J., Gaudet, P and de Lorenzo, V.
Opublikowane w: Frontiers in Physiology, Numer 1664042X, 2022, ISSN 1664-042X
Wydawca: Frontiers Research Foundation
DOI: 10.3389/fphys.2022.815874

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

Autorzy: 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
Opublikowane w: Microbial Biotechnology, 2020, ISSN 1751-7915
Wydawca: Society for applied Microbiology
DOI: 10.1111/1751-7915.13675

Optimizing yeast for high-level production of kaempferol and quercetin

Autorzy: Musa Tartik, Juan Liu, Marta Tous Mohedano, Jiwei Mao, Yun Chen
Opublikowane w: Microbial Cell Factories, 2023, ISSN 1475-2859
Wydawca: 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.

Autorzy: 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.
Opublikowane w: Nucleic Acids Research, 2023, ISSN 1362-4962
Wydawca: Oxford University Press
DOI: 10.1093/nar/gkad758

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

Autorzy: Nikel, P.I., Benedetti, I., Wirth, N.T., de Lorenzo, V. and Calles, B.
Opublikowane w: Microbial Biotechnology, Numer 17517915, 2022, ISSN 1751-7915
Wydawca: John Wiley and Sons
DOI: 10.1111/1751-7915.14063

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

Autorzy: Tobias Goris, Annett Braune
Opublikowane w: Abstract Book - International Conference on Polyphenols, 2022
Wydawca: ICPH Conference

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

Autorzy: Angeles Hueso-Gil; Victor de Lorenzo; Akos Nyerges
Opublikowane w: bioRxiv, 2019
Wydawca: Cold Spring Harbor Laboratory
DOI: 10.1101/771782

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

Autorzy: Pavel Dvořák; Edward A. Bayer; Víctor de Lorenzo
Opublikowane w: bioRxiv, 2020
Wydawca: Cold Spring Harbor Laboratory
DOI: 10.1101/2020.05.13.093500

Metabolic Modelling Approaches for Describing and Engineering Microbial Communities

Autorzy: Beatriz García-Jiménez , Jesús Torres, Juan Nogales
Opublikowane w: 2020
Wydawca: Preprints
DOI: 10.20944/preprints202009.0548.v1

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

Autorzy: San León Granado, David; Blázquez, Blas; Nogales, Juan
Opublikowane w: International Journal of Molecular Sciences, Numer 37, 2023, ISSN 1422-0067
Wydawca: MDPI
DOI: 10.5281/zenodo.8171332

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

Autorzy: Suhui Ye, Patricia Magadán-Corpas, Álvaro Pérez-Valero, Jesús Torres-Bacete, Juan Nogales, Claudio J. Villar, Felipe Lombó
Opublikowane w: 2022
Wydawca: 3rd Synthetic Biology of Natural Products Conference

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

Autorzy: Álvaro Pérez-Valero, Suhui Ye, Patricia Magadán-Corpas, Claudio J. Villar, Felipe Lombó
Opublikowane w: 2022
Wydawca: 3rd Synthetic Biology of Natural Products Conference

Improvement in flavonoids production combining different strategies

Autorzy: Patricia Magadán-Corpas, Suhui Ye, Álvaro Pérez-Valero, Claudio J. Villar, Felipe Lombó
Opublikowane w: 2022
Wydawca: 3rd Synthetic Biology of Natural Products Conference

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

Autorzy: Molly Hogle, Barbara Imhof, Waltraut Hoheneder, Rachel Armstrong, Ioannis Ieropoulos, Lauren Wallis, Jiseon You, Juan Nogales. Ed. Peter Droege
Opublikowane w: Urban and Regional Agriculture. Building Resilient Food Systems, 2023, ISBN 9780128202869
Wydawca: 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.

Autorzy: Aparicio T., de Lorenzo V., Martínez-García E.
Opublikowane w: Horizontal Gene Transfer, 2019, ISBN 978-1-4939-9877-7
Wydawca: Humana, New York
DOI: 10.1007/978-1-4939-9877-7_27

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

Autorzy: Aparicio, T., de Lorenzo, V., Martínez-García, E.
Opublikowane w: Methods in Molecular Biology, 2022, ISBN 978-1-0716-2232-2
Wydawca: Humana
DOI: 10.1007/978-1-0716-2233-9_4

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

Autorzy: 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
Opublikowane w: bioRxiv, Numer 26928205, 2022, ISSN 2692-8205
Wydawca: Cold Spring Harbor Laboratory
DOI: 10.1101/2022.09.20.508659

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