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

Información del proyecto

EmPowerPutida

Identificador del acuerdo de subvención: 635536

DOI

10.3030/635536

Proyecto cerrado

Fecha de la firma de la CE 13 Marzo 2015

Fecha de inicio 1 Mayo 2015

Fecha de finalización 30 Abril 2019

Financiado con arreglo a

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

Coste total

€ 6 839 673,00

Aportación de la UE

€ 6 020 825,00

Coordinado por

WAGENINGEN UNIVERSITY
Netherlands

CORDIS proporciona enlaces a los documentos públicos y las publicaciones de los proyectos de los programas marco HORIZONTE.

Los enlaces a los documentos y las publicaciones de los proyectos del Séptimo Programa Marco, así como los enlaces a algunos tipos de resultados específicos, como conjuntos de datos y «software», se obtienen dinámicamente de OpenAIRE .

Resultado final

Documents, reports (2)

White Paper

White Paper on outcomes and best practices relating to safety and risk assessment aspects of EmPowerPutida

sRNA regulators for post-transcriptional control

Report of on the first set of sRNA regulators for posttranscriptional control of gene expression and modulation of protein production in P putida

Websites, patent fillings, videos etc. (3)

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)

Demonstrators, pilots, prototypes (3)

(post-)Transcriptional genetic devices

A suite of ca 5 transcriptionposttranscription genetic devices for complete and reversible shutdown 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

Publicaciones

Peer reviewed articles (23)

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

Autores: Jasper J. Koehorst, Edoardo Saccenti, Peter J. Schaap, Vitor A. P. Martins dos Santos, Maria Suarez-Diez
Publicado en: F1000Research, Edición 5, 2016, Página(s) 1987, ISSN 2046-1402
Editor: F1000 Research Ltd.
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

Autores: Aitor de las Heras, Esteban Martínez-García, Maria Rosa Domingo-Sananes, Sofia Fraile, Víctor de Lorenzo
Publicado en: Integr. Biol., Edición 8/4, 2016, Página(s) 571-576, ISSN 1757-9694
Editor: Royal Society of Chemistry
DOI: 10.1039/C5IB00310E

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

Autores: Pablo I. Nikel, Danilo Pérez-Pantoja, Víctor de Lorenzo
Publicado en: Environmental Microbiology, Edición 18/10, 2016, Página(s) 3565-3582, ISSN 1462-2912
Editor: Blackwell Publishing Inc.
DOI: 10.1111/1462-2920.13434

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

Autores: Juhyun Kim, Danilo Pérez-Pantoja, Rafael Silva-Rocha, Juan Carlos Oliveros, Víctor de Lorenzo
Publicado en: Environmental Microbiology, Edición 18/10, 2016, Página(s) 3327-3341, ISSN 1462-2912
Editor: Blackwell Publishing Inc.
DOI: 10.1111/1462-2920.13054

Physical Forces Shape Group Identity of Swimming Pseudomonas putida Cells

Autores: David R. Espeso, Esteban Martínez-García, Víctor de Lorenzo, Ángel Goñi-Moreno
Publicado en: Frontiers in Microbiology, Edición 7, 2016, ISSN 1664-302X
Editor: Frontiers Media
DOI: 10.3389/fmicb.2016.01437

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

Autores: Víctor de Lorenzo, Philippe Marlière, Ricard Solé
Publicado en: Microbial Biotechnology, Edición 9/5, 2016, Página(s) 618-625, ISSN 1751-7915
Editor: Microb Biotechnol.
DOI: 10.1111/1751-7915.12399

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

Autores: Ilaria Benedetti, Víctor de Lorenzo, Pablo I. Nikel
Publicado en: Metabolic Engineering, Edición 33, 2016, Página(s) 109-118, ISSN 1096-7176
Editor: Academic Press
DOI: 10.1016/j.ymben.2015.11.004

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

Autores: Alejandro Arce-Rodríguez, Belén Calles, Pablo I. Nikel, Víctor de Lorenzo
Publicado en: Environmental Microbiology, Edición 18/10, 2016, Página(s) 3309-3326, ISSN 1462-2912
Editor: Blackwell Publishing Inc.
DOI: 10.1111/1462-2920.13052

The quest for the minimal bacterial genome

Autores: Esteban Martínez-García, Víctor de Lorenzo
Publicado en: Current Opinion in Biotechnology, Edición 42, 2016, Página(s) 216-224, ISSN 0958-1669
Editor: Elsevier BV
DOI: 10.1016/j.copbio.2016.09.001

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

Autores: Markus Schmidt, Víctor de Lorenzo
Publicado en: Current Opinion in Biotechnology, Edición 38, 2016, Página(s) 90-96, ISSN 0958-1669
Editor: Elsevier BV
DOI: 10.1016/j.copbio.2016.01.006

The Ssr protein (T1E_1405) from Pseudomonas putida DOT-T1E enables oligonucleotide-based recombineering in platform strain P. putida EM42

Autores: Tomás Aparicio, Sheila I. Jensen, Alex T. Nielsen, Victor de Lorenzo, Esteban Martínez-García
Publicado en: Biotechnology Journal, Edición 11/10, 2016, Página(s) 1309-1319, ISSN 1860-6768
Editor: Wiley - VCH Verlag GmbH & CO. KGaA
DOI: 10.1002/biot.201600317

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

Autores: Raúl Guantes, Ilaria Benedetti, Rafael Silva-Rocha, Víctor de Lorenzo
Publicado en: The ISME Journal, Edición 10/5, 2015, Página(s) 1122-1133, ISSN 1751-7362
Editor: Nature Publishing Group
DOI: 10.1038/ismej.2015.193

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

Autores: Ilaria Benedetti, Pablo I. Nikel, Víctor de Lorenzo
Publicado en: Data in Brief, Edición 6, 2016, Página(s) 738-744, ISSN 2352-3409
Editor: Elsevier BV
DOI: 10.1016/j.dib.2016.01.022

Asymmetric Enzymatic Hydration of Unactivated, Aliphatic Alkenes

Autores: Rebecca M. Demming, Stephan C. Hammer, Bettina M. Nestl, Sebastian Gergel, Silvia Fademrecht, Jürgen Pleiss, Bernhard Hauer
Publicado en: Angewandte Chemie International Edition, 2018, ISSN 1433-7851
Editor: John Wiley & Sons Ltd.
DOI: 10.1002/anie.201810005

Pseudomonas putida KT 2440 is HV 1 certified, not GRAS

Autores: Linde F. C. Kampers, Rita J. M. Volkers, Vitor A. P. Martins dos Santos
Publicado en: Microbial Biotechnology, 2019, ISSN 1751-7915
Editor: wiley
DOI: 10.1111/1751-7915.13443

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

Autores: Nhung Pham, Ruben van Heck, Jesse van Dam, Peter Schaap, Edoardo Saccenti, Maria Suarez-Diez
Publicado en: Metabolites, Edición 9/2, 2019, Página(s) 28, ISSN 2218-1989
Editor: MDPI
DOI: 10.3390/metabo9020028

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

Autores: 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
Publicado en: Microbial Cell Factories, Edición 18/1, 2019, ISSN 1475-2859
Editor: BioMed Central
DOI: 10.1186/s12934-019-1227-5

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

Autores: Sanjeevan Jahagirdar, Maria Suarez-Diez, Edoardo Saccenti
Publicado en: Journal of Proteome Research, Edición 18/3, 2019, Página(s) 1099-1113, ISSN 1535-3893
Editor: American Chemical Society
DOI: 10.1021/acs.jproteome.8b00781

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

Autores: Jesse C. J. van Dam, Jasper J. Koehorst, Jon Olav Vik, Vitor A. P. Martins dos Santos, Peter J. Schaap, Maria Suarez-Diez
Publicado en: Scientific Data, Edición 6/1, 2019, ISSN 2052-4463
Editor: nature journals
DOI: 10.1038/s41597-019-0263-7

SyNDI: synchronous network data integration framework

Autores: Erno Lindfors, Jesse C. J. van Dam, Carolyn Ming Chi Lam, Niels A. Zondervan, Vitor A. P. Martins dos Santos, Maria Suarez-Diez
Publicado en: BMC Bioinformatics, Edición 19/1, 2018, ISSN 1471-2105
Editor: BioMed Central
DOI: 10.1186/s12859-018-2426-5

Structural and functional insights into asymmetric enzymatic dehydration of alkenols

Autores: 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
Publicado en: Nature Chemical Biology, Edición 13/3, 2017, Página(s) 275-281, ISSN 1552-4450
Editor: Nature Publishing Group
DOI: 10.1038/nchembio.2271

Optimized Reaction Conditions Enable the Hydration of Non-natural Substrates by the Oleate Hydratase from Elizabethkingia meningoseptica

Autores: Rebecca M. Demming, Konrad B. Otte, Bettina M. Nestl, Bernhard Hauer
Publicado en: ChemCatChem, Edición 9/5, 2017, Página(s) 758-766, ISSN 1867-3880
Editor: Wiley - VCH Verlag GmbH & CO. KGaA
DOI: 10.1002/cctc.201601329

Inside Cover: Optimized Reaction Conditions Enable the Hydration of Non-natural Substrates by the Oleate Hydratase from Elizabethkingia meningoseptica (ChemCatChem 5/2017)

Autores: Rebecca M. Demming, Konrad B. Otte, Bettina M. Nestl, Bernhard Hauer
Publicado en: ChemCatChem, Edición 9/5, 2017, Página(s) 716-716, ISSN 1867-3880
Editor: Wiley - VCH Verlag GmbH & CO. KGaA
DOI: 10.1002/cctc.201700258

Book chapters (4)

Introduction to Genetic, Genomic and System Analyses of Pure Cultures

Autores: Víctor de Lorenzo
Publicado en: Hydrocarbon and Lipid Microbiology Protocols, 2017, Página(s) 1-7, ISBN 978-3-662-50435-2
Editor: Springer Berlin Heidelberg
DOI: 10.1007/8623_2016_192

Systems and Synthetic Biology in Hydrocarbon Microbiology: Tools

Autores: Víctor de Lorenzo
Publicado en: Hydrocarbon and Lipid Microbiology Protocols, 2016, Página(s) 1-7, ISBN 978-3-662-50432-1
Editor: Springer Berlin Heidelberg
DOI: 10.1007/8623_2015_185

Engineering Gram-Negative Microbial Cell Factories Using Transposon Vectors

Autores: Esteban Martínez-García, Tomás Aparicio, Víctor de Lorenzo, Pablo I. Nikel
Publicado en: In Vitro Mutagenesis, 2017, Página(s) 273-293, ISBN 978-1-4939-6472-7
Editor: Springer New York
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

Autores: Belén Calles, Víctor de Lorenzo
Publicado en: Hydrocarbon and Lipid Microbiology Protocols, 2017, Página(s) 71-85, ISBN 978-3-662-50435-2
Editor: Springer Berlin Heidelberg
DOI: 10.1007/8623_2015_114

Thesis and dissertations (1)

Metabolic modeling to understand and redesign microbial systems

Autores: Ruben van Heck
Publicado en: Thesis, 2017, ISBN 9789-463434553
Editor: Wageningen University & Research