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Exploiting native endowments by re-factoring, re-programming and implementing novel control loops in Pseudomonas putida for bespoke biocatalysis

Deliverables

Website & communication pipeline

Website and internal communication structure established

Public Dialogue

Report on the public dialogue activities, briefing material for scientists

SOPs

Publication of SOPs (internal and SOPs open to the public)

(post-)Transcriptional genetic devices

A suite of ca 5 transcription/post-transcription genetic devices for complete and reversible shut-down or full activation of functions determining growth and stasis

Genome Edited P. Putida

One P. putida strain with a deeply edited and enhanced genome as the host of up to ten insertions of genetic devices in stable and transcriptionally able sites of the chromosome

Short-chain alcohols-resistant Pseudomonas strains

Short chain alcohols resistant Pseudomonas strains

sRNA regulators for post-transcriptional control

Report of on the first set of sRNA regulators for post-transcriptional control of gene expression and modulation of protein production in P. putida .

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Publications

Protein domain architectures provide a fast, efficient and scalable alternative to sequence-based methods for comparative functional genomics

Author(s): Jasper J. Koehorst, Edoardo Saccenti, Peter J. Schaap, Vitor A. P. Martins dos Santos, Maria Suarez-Diez
Published in: F1000Research, Issue 5, 2016, Page(s) 1987, ISSN 2046-1402
DOI: 10.12688/f1000research.9416.3

Rationally rewiring the connectivity of the XylR/Pu regulatory node of the m-xylene degradation pathway in Pseudomonas putida

Author(s): Aitor de las Heras, Esteban Martínez-García, Maria Rosa Domingo-Sananes, Sofia Fraile, Víctor de Lorenzo
Published in: Integr. Biol., Issue 8/4, 2016, Page(s) 571-576, ISSN 1757-9694
DOI: 10.1039/C5IB00310E

Pyridine nucleotide transhydrogenases enable redox balance of Pseudomonas putida during biodegradation of aromatic compounds

Author(s): Pablo I. Nikel, Danilo Pérez-Pantoja, Víctor de Lorenzo
Published in: Environmental Microbiology, Issue 18/10, 2016, Page(s) 3565-3582, ISSN 1462-2912
DOI: 10.1111/1462-2920.13434

High-resolution analysis of the m -xylene/toluene biodegradation subtranscriptome of P seudomonas putida mt-2

Author(s): Juhyun Kim, Danilo Pérez-Pantoja, Rafael Silva-Rocha, Juan Carlos Oliveros, Víctor de Lorenzo
Published in: Environmental Microbiology, Issue 18/10, 2016, Page(s) 3327-3341, ISSN 1462-2912
DOI: 10.1111/1462-2920.13054

Physical Forces Shape Group Identity of Swimming Pseudomonas putida Cells

Author(s): David R. Espeso, Esteban Martínez-García, Víctor de Lorenzo, Ángel Goñi-Moreno
Published in: Frontiers in Microbiology, Issue 7, 2016, ISSN 1664-302X
DOI: 10.3389/fmicb.2016.01437

Bioremediation at a global scale: from the test tube to planet Earth

Author(s): Víctor de Lorenzo, Philippe Marlière, Ricard Solé
Published in: Microbial Biotechnology, Issue 9/5, 2016, Page(s) 618-625, ISSN 1751-7915
DOI: 10.1111/1751-7915.12399

Genetic programming of catalytic Pseudomonas putida biofilms for boosting biodegradation of haloalkanes

Author(s): Ilaria Benedetti, Víctor de Lorenzo, Pablo I. Nikel
Published in: Metabolic Engineering, Issue 33, 2016, Page(s) 109-118, ISSN 1096-7176
DOI: 10.1016/j.ymben.2015.11.004

The RNA chaperone Hfq enables the environmental stress tolerance super-phenotype of P seudomonas putida

Author(s): Alejandro Arce-Rodríguez, Belén Calles, Pablo I. Nikel, Víctor de Lorenzo
Published in: Environmental Microbiology, Issue 18/10, 2016, Page(s) 3309-3326, ISSN 1462-2912
DOI: 10.1111/1462-2920.13052

The quest for the minimal bacterial genome

Author(s): Esteban Martínez-García, Víctor de Lorenzo
Published in: Current Opinion in Biotechnology, Issue 42, 2016, Page(s) 216-224, ISSN 0958-1669
DOI: 10.1016/j.copbio.2016.09.001

Synthetic bugs on the loose: containment options for deeply engineered (micro)organisms

Author(s): Markus Schmidt, Víctor de Lorenzo
Published in: Current Opinion in Biotechnology, Issue 38, 2016, Page(s) 90-96, ISSN 0958-1669
DOI: 10.1016/j.copbio.2016.01.006

Transcription factor levels enable metabolic diversification of single cells of environmental bacteria

Author(s): Raúl Guantes, Ilaria Benedetti, Rafael Silva-Rocha, Víctor de Lorenzo
Published in: The ISME Journal, Issue 10/5, 2015, Page(s) 1122-1133, ISSN 1751-7362
DOI: 10.1038/ismej.2015.193

Data on the standardization of a cyclohexanone-responsive expression system for Gram-negative bacteria

Author(s): Ilaria Benedetti, Pablo I. Nikel, Víctor de Lorenzo
Published in: Data in Brief, Issue 6, 2016, Page(s) 738-744, ISSN 2352-3409
DOI: 10.1016/j.dib.2016.01.022

Asymmetric Enzymatic Hydration of Unactivated, Aliphatic Alkenes


Published in: ISSN 1433-7851
DOI: 10.1002/anie.201810005

Pseudomonas putida KT 2440 is HV 1 certified, not GRAS

Author(s): Linde F. C. Kampers, Rita J. M. Volkers, Vitor A. P. Martins dos Santos
Published in: Microbial Biotechnology, 2019, ISSN 1751-7915
DOI: 10.1111/1751-7915.13443

Consistency, Inconsistency, and Ambiguity of Metabolite Names in Biochemical Databases Used for Genome-Scale Metabolic Modelling

Author(s): Nhung Pham, Ruben van Heck, Jesse van Dam, Peter Schaap, Edoardo Saccenti, Maria Suarez-Diez
Published in: Metabolites, Issue 9/2, 2019, Page(s) 28, ISSN 2218-1989
DOI: 10.3390/metabo9020028

In silico-guided engineering of Pseudomonas putida towards growth under micro-oxic conditions

Author(s): Linde F. C. Kampers, Ruben G. A. van Heck, Stefano Donati, Edoardo Saccenti, Rita J. M. Volkers, Peter J. Schaap, Maria Suarez-Diez, Pablo I. Nikel, Vitor A. P. Martins dos Santos
Published in: Microbial Cell Factories, Issue 18/1, 2019, ISSN 1475-2859
DOI: 10.1186/s12934-019-1227-5

Simulation and Reconstruction of Metabolite–Metabolite Association Networks Using a Metabolic Dynamic Model and Correlation Based Algorithms

Author(s): Sanjeevan Jahagirdar, Maria Suarez-Diez, Edoardo Saccenti
Published in: Journal of Proteome Research, Issue 18/3, 2019, Page(s) 1099-1113, ISSN 1535-3893
DOI: 10.1021/acs.jproteome.8b00781

The Empusa code generator and its application to GBOL, an extendable ontology for genome annotation

Author(s): Jesse C. J. van Dam, Jasper J. Koehorst, Jon Olav Vik, Vitor A. P. Martins dos Santos, Peter J. Schaap, Maria Suarez-Diez
Published in: Scientific Data, Issue 6/1, 2019, ISSN 2052-4463
DOI: 10.1038/s41597-019-0263-7

SyNDI: synchronous network data integration framework

Author(s): Erno Lindfors, Jesse C. J. van Dam, Carolyn Ming Chi Lam, Niels A. Zondervan, Vitor A. P. Martins dos Santos, Maria Suarez-Diez
Published in: BMC Bioinformatics, Issue 19/1, 2018, ISSN 1471-2105
DOI: 10.1186/s12859-018-2426-5

Structural and functional insights into asymmetric enzymatic dehydration of alkenols

Author(s): Bettina M Nestl, Christopher Geinitz, Stephanie Popa, Sari Rizek, Robert J Haselbeck, Rosary Stephen, Michael A Noble, Max-Philipp Fischer, Erik C Ralph, Hoi Ting Hau, Henry Man, Muhiadin Omar, Johan P Turkenburg, Stephen van Dien, Stephanie J Culler, Gideon Grogan, Bernhard Hauer
Published in: Nature Chemical Biology, Issue 13/3, 2017, Page(s) 275-281, ISSN 1552-4450
DOI: 10.1038/nchembio.2271

Introduction to Genetic, Genomic and System Analyses of Pure Cultures

Author(s): Víctor de Lorenzo
Published in: Hydrocarbon and Lipid Microbiology Protocols, 2017, Page(s) 1-7
DOI: 10.1007/8623_2016_192

Systems and Synthetic Biology in Hydrocarbon Microbiology: Tools

Author(s): Víctor de Lorenzo
Published in: Hydrocarbon and Lipid Microbiology Protocols, 2016, Page(s) 1-7
DOI: 10.1007/8623_2015_185

Engineering Gram-Negative Microbial Cell Factories Using Transposon Vectors

Author(s): Esteban Martínez-García, Tomás Aparicio, Víctor de Lorenzo, Pablo I. Nikel
Published in: In Vitro Mutagenesis, 2017, Page(s) 273-293
DOI: 10.1007/978-1-4939-6472-7_18

Knock-In-Leave-Behind (KILB): Genetic Grafting of Protease-Cleaving Sequences into Permissive Sites of Proteins with a Tn5-Based Transposition System

Author(s): Belén Calles, Víctor de Lorenzo
Published in: Hydrocarbon and Lipid Microbiology Protocols, 2017, Page(s) 71-85
DOI: 10.1007/8623_2015_114

Metabolic modeling to understand and redesign microbial systems