Papers and articles

List of project publications

Subcellular Architecture of the xyl Gene Expression Flow of the TOL Catabolic Plasmid of Pseudomonas putida mt-2
Juhyun Kim, Angel Goñi-Moreno, Víctor de Lorenzo
Peer-review article in mBio, published online 23 February 2021, American Society for Microbiology
Open Access – Green OA
https://doi.org/10.1128/mbio.03685-20

Low CyaA expression and anticooperative binding of cAMP to CRP frames the scope of the cognate regulon of Pseudomonas putida
Alejandro ArceRodríguez, Pablo I. Nikel, Belén Calles, Max Chavarría, Raúl Platero, Tino Krell, Victor de Lorenzo
Peer-review article in Environmental Microbiology, Early View, first published: 8 February 2021. Society for Applied Microbiology and John Wiley & Sons Ltd., UK.
Open Access – Green OA
https://doi.org/10.1111/1462-2920.15422

For the sake of the Bioeconomy: define what a Synthetic Biology Chassis is!
Víctor de Lorenzo, Natalio Krasnogor, Markus Schmidt
Peer-review article in New Biotechnology, 60, published: 25 January 2021, Elsevier BV
Open Access – Green OA
https://doi.org/10.1016/j.nbt.2020.08.004

Contextual dependencies expand the re-usability of genetic inverters
Huseyin Tas, Lewis Grozinger, Ruud Stoof, Victor de Lorenzo, Ángel Goñi-Moreno
Peer-review article in Nature Communications, 12/1, 2021, published: 13 January 2021, Springer Nature
Open Access – Green OA
https://doi.org/10.1038/s41467-020-20656-5

Reconfiguration of metabolic fluxes in Pseudomonas putida as a response to sub-lethal oxidative stress
Pablo I. Nikel, Tobias Fuhrer, Max Chavarría, Alberto Sánchez-Pascuala, Uwe Sauer & Victor de Lorenzo
Peer-review article in The ISME Journal, 2021, published: 11 January 2021, Springer Nature
Open Access – Gold OA
https://doi.org/10.1038/s41396-020-00884-9

The faulty SOS response of Pseudomonas putida KT2440 stems from an inefficient RecA-LexA interplay
Özlem Akkaya, Tomás Aparicio, Danilo PérezPantoja, Víctor de Lorenzo
Peer-review article in Environmental Microbiology, Early view, first published: 3 January 2021, Society for Applied Microbiology and John Wiley & Sons Ltd
Open Access – Green OA
https://doi.org/10.1111/1462-2920.15384

In vivo diversification of target genomic sites using processive base deaminase fusions blocked by dCas9
Beatriz Álvarez, Mario Mencía, Víctor de Lorenzo, Luis Ángel Fernández
Peer-review article in Nature Communications, 11 /1, 2020, published: 22 December 2020, Springer Nature
Open Access – Green OA
https://doi.org/10.1038/s41467-020-20230-z

A Standardized Inverter Package Borne by Broad Host Range Plasmids for Genetic Circuit Design in Gram-Negative Bacteria
Huseyin Tas, Ángel Goñi-Moreno, Víctor de Lorenzo
Peer-review article in ACS Synthetic Biology, 10/1, 2020, published: 18 December 2020. American Chemical Society
Open Access – Gold OA
https://doi.org/10.1021/acssynbio.0c00529

Concomitant prediction of environmental fate and toxicity of chemical compounds
Juan Antonio Garcia-Martin, Max Chavarría, Victor de Lorenzo, Florencio Pazos
Peer-review article in Biology Methods and Protocols, 5/1, 2020, published: 13 November 2020, Oxford Academic
Open Access – Gold OA
https://doi.org/10.1093/biomethods/bpaa025

Repositioning microbial biotechnology against COVID19: the case of microbial production of flavonoids
Tobias Goris, Álvaro PérezValero, Igor Martínez, Dong Yi, Luis FernándezCalleja, David San León, Uwe T. Bornscheuer, Patricia MagadánCorpas, Felipe Lombó, Juan Nogales
Peer-review article in Microbial Biotechnology, 14/ 1, 2021, first published: 13 October 2020, Society for Applied Microbiology and John Wiley & Sons Ltd
Open Access – Gold OA
https://doi.org/10.1111/1751-7915.13675

An automated DIY framework for experimental evolution of Pseudomonas putida
David R. Espeso, Pavel Dvořák, Tomás Aparicio, Víctor de Lorenzo
Peer-review article in Microbial Biotechnology, Online Version of Record before inclusion in an issue, first published: 13 October 2020, Society for Applied Microbiology and John Wiley & Sons Ltd
Open Access – Gold OA
https://doi.org/10.1111/1751-7915.13678

Quantitative assessment of morphological traits of planktonic bacterial aggregates
David R. Espeso, Esteban Martínez-García, Víctor de Lorenzo
Peer-review article in Water Research, Volume 188, 1 January 2021, first published: 28 September 2020, Elsevier BV
https://doi.org/10.1016/j.watres.2020.116468

Metabolic Modelling Approaches for Describing and Engineering Microbial Communities
Beatriz García-Jiménez, Jesús Torres, Juan Nogales
Peer-review article in Computational and Structural Biotechnology Journal, 19, 2021, first published in Preprints, 23 September 2020, MDPI AG
Open Access – Gold OA
https://doi.org/10.1016/j.csbj.2020.12.003
https://doi.org/10.20944/preprints202009.0548.v


Surface display of designer protein scaffolds on genome-reduced strains of Pseudomonas putida
Pavel Dvořák, Edward A. Bayer, Víctor de Lorenzo
Research article in ACS Synthetic Biology, 2020, 9/10, 2 September 2020, American Chemical Society
Open Access – Gold OA
https://doi.org/10.1021/acssynbio.0c00276

Environmental Performance of Pseudomonas putida with a Uracylated Genome
Elena Algar, Yamal AlRamahi, Víctor de Lorenzo, Esteban MartínezGarcía
Peer-review article in ChemBioChem, 21/22, 2020, first published: 29 June 2020, Wiley Online Library
Open Access – Gold OA
https://doi.org/10.1002/cbic.202000330

Naked Bacterium: Emerging Properties of a Surfome-Streamlined Pseudomonas putida Strain
Esteban Martínez-García, Sofía Fraile, David Rodríguez Espeso, Davide Vecchietti, Giovanni Bertoni, Víctor de Lorenzo
Peer-review article in ACS Synthetic Biology, 2020, 9/9, 30 July 2020, American Chemical Society
Open Access – Green OA
https://doi.org/10.1021/acssynbio.0c00272

A SsrA/NIa-based Strategy for Post-Translational Regulation of Protein Levels in Gram-negative Bacteria
Gonzalo Durante-Rodríguez, Belén Calles, Víctor de Lorenzo, Pablo Nikel
Peer-review article in BIO-PROTOCOL, 10/14, July 2020. Bio-Protocol, LLC
Open Access – Gold OA
https://doi.org/10.21769/bioprotoc.3688

The Wsp intermembrane complex mediates metabolic control of the swimattach decision of Pseudomonas putida
Ángeles HuesoGil, Belén Calles, Víctor de Lorenzo
Peer-review article in Environmental Microbiology, Volume 22, Issue 8, August 2020, first published: 9 June 2020, Society for Applied Microbiology and John Wiley & Sons Ltd.
Open Access – Green OA
https://doi.org/10.1111/1462-2920.15126

Exploiting geometric similarity for statistical quantification of fluorescence spatial patterns in bacterial colonies
David R. Espeso, Elena Algar, Esteban Martínez-García, Víctor de Lorenzo
Peer-review article in BMC Bioinformatics, 21, 3 June 2020, Springer Nature
Open Access – Green OA
https://doi.org/10.1186/s12859-020-3490-1

Targeted Depletion of Bacteria from Mixed Populations by Programmable Adhesion with Antagonistic Competitor Cells
See-Yeun Ting, Esteban Martínez-García, Shuo Huang, Savannah K. Bertolli, Katherine A. Kelly, Kevin J. Cutler, Elizabeth D. Su, Hui Zhi, Qing Tang, Matthew C. Radey, Manuela Raffatellu, S. Brook Peterson, Víctor de Lorenzo, Joseph D. Mougou
Peer-review article in Cell Host & Microbe, 28/2, August 2020, first published: 28 May 2020, Elsevier BV
Open Access – Green OA
https://doi.org/10.1016/j.chom.2020.05.006

Biotransformation of Dxylose to Dxylonate coupled to mediumchainlength polyhydroxyalkanoate production in cellobiosegrown Pseudomonas putida EM42
Pavel Dvořák, Jozef Kováč, Víctor de Lorenzo
Peer-review article in Microbial Biotechnology, 13/4, July 2020, first published: 3 May 2020, Society for Applied Microbiology and John Wiley & Sons Ltd
Open Access -Green OA
https://doi.org/10.1111/1751-7915.13574

ArsH protects Pseudomonas putida from oxidative damage caused by exposure to arsenic
A. David PáezEspino, Pablo I. Nikel, Max Chavarría, Víctor de Lorenzo
Peer-review article in Environmental Microbiology, 22/ 6, June 2020, first published: 23 March 2020, Society for Applied Microbiology and John Wiley & Sons Ltd
Open Access – Green OA
https://doi.org/10.1111/1462-2920.14991

Multifunctional SEVA shuttle vectors for actinomycetes and Gramnegative bacteria
Coral GarcíaGutiérrez, Tomás Aparicio, Lucía TorresSánchez, Esteban MartínezGarcía, Víctor Lorenzo, Claudio J. Villar, Felipe Lombó
Peer-review article in MicrobiologyOpen, Volume 9, Issue 6, June 2020, first published: 14 March 2020, John Wiley & Sons Ltd
Open Access – Gold OA
https://doi.org/10.1002/mbo3.1024

High-Efficiency Multi-site Genomic Editing of Pseudomonas putida through Thermoinducible ssDNA Recombineering.
Tomas Aparicio, Akos Nyerges, Esteban Martínez-García, Víctor de Lorenzo
Peer-review article in iScience, 23/ 3, March 2020, first published: 26 February 2020, Elsevier BV
Open Access – Gold OA
https://doi.org/10.1016/j.isci.2020.100946

SEVA 3.0: an update of the Standard European Vector Architecture for enabling portability of genetic constructs among diverse bacterial hosts
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
Peer-review article in Nucleic Acids Research, 48/ D1, 8 January 2020, first published: 19 November 2019. Oxford University Press
Open Access -Gold OA
https://doi.org/10.1093/nar/gkz1024

Digitalizing heterologous gene expression in Gramnegative bacteria with a portable ON/OFF module
Belén Calles, Ángel GoñiMoreno, Víctor Lorenzo
Peer-review article in Molecular Systems Biology, 15/ 12, 19 December 2019, EMBO
Open Access – Gold OA
https://doi.org/10.15252/msb.20188777

Multiple-Site Diversification of Regulatory Sequences Enables Interspecies Operability of Genetic Devices
Angeles Hueso-Gil, Ákos Nyerges, Csaba Pál, Belén Calles, Víctor de Lorenzo
Peer-review article in ACS Synthetic Biology, 9/1, 03 December 2019, American Chemical Society
Open Access – Gold OA
https://doi.org/10.1021/acssynbio.9b00375

Using synthetic biology for flavonoid production
Juan Nogales
Q&A Session with Juan Nogales in SynGen Series, October 2019, Oxford Global
https://www.oxfordglobal.co.uk/wp-content/uploads/2019/10/QA-Juan-Nogales.pdf

Highquality genomescale metabolic modelling of Pseudomonas putida highlights its broad metabolic capabilities
Juan Nogales, Joshua Mueller, Steinn Gudmundsson, Francisco J. Canalejo, Estrella Duque, Jonathan Monk, Adam M. Feist, Juan Luis Ramos, Wei Niu, Bernhard O. Palsson
Peer-review article in Environmental Microbiology, 22/1 January 2020, first published: 27 October 2019, Society for Applied Microbiology and John Wiley & Sons Ltd
Open Access -Gold OA
https://doi.org/10.1111/1462-2920.14843

Mismatch repair hierarchy of Pseudomonas putida revealed by mutagenic ssDNA recombineering of the pyrF gene
Tomas Aparicio, Akos Nyerges, István Nagy, Csaba Pal, Esteban MartínezGarcía, Víctor Lorenzo
Peer-review article in Environmental Microbiology, 22 /1, January 2020, first published: 09 October 2019, Society for Applied Microbiology and John Wiley & Sons Ltd
Open Access – Gold OA
https://doi.org/10.1111/1462-2920.14814

A Broad Host Range Plasmid-Based Roadmap for ssDNA-Based Recombineering in Gram-Negative Bacteria
Tomás Aparicio, Víctor de Lorenzo, Esteban Martínez-García
Peer-review article in Horizontal Gene Transfer, first online: 05 October 2019, Springer Nature
Open Access – Green OA
https://doi.org/10.1007/978-1-4939-9877-7_27

Recombination-Independent Genome Editing through CRISPR/Cas9-Enhanced TargeTron Delivery
Elena Velázquez, Víctor de Lorenzo, Yamal Al-Ramahi
Peer-review article in ACS Synthetic Biology, 8/9, 16 August 2019, American Chemical Society
Open Access – Green OA
https://doi.org/10.1021/acssynbio.9b00293

Functional implementation of a linear glycolysis for sugar catabolism in Pseudomonas putida
Alberto Sánchez-Pascuala, Lorena Fernández-Cabezón, Víctor de Lorenzo, Pablo I. Nikel
Peer-review article in Metabolic Engineering, Volume 54, July 2019, Elsevier BV
Open Access – Green OA
https://doi.org/10.1016/j.ymben.2019.04.005