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

Informazioni relative al progetto

EmPowerPutida

ID dell’accordo di sovvenzione: 635536

DOI

10.3030/635536

Progetto chiuso

Data della firma CE 13 Marzo 2015

Data di avvio 1 Maggio 2015

Data di completamento 30 Aprile 2019

Finanziato da

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

Costo totale

€ 6 839 673,00

Contributo UE

€ 6 020 825,00

Coordinato da

WAGENINGEN UNIVERSITY
Netherlands

CORDIS fornisce collegamenti ai risultati finali pubblici e alle pubblicazioni dei progetti ORIZZONTE.

I link ai risultati e alle pubblicazioni dei progetti del 7° PQ, così come i link ad alcuni tipi di risultati specifici come dataset e software, sono recuperati dinamicamente da .OpenAIRE .

Risultati finali

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

Pubblicazioni

Peer reviewed articles (23)

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

Autori: Jasper J. Koehorst, Edoardo Saccenti, Peter J. Schaap, Vitor A. P. Martins dos Santos, Maria Suarez-Diez
Pubblicato in: F1000Research, Numero 5, 2016, Pagina/e 1987, ISSN 2046-1402
Editore: 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

Autori: Aitor de las Heras, Esteban Martínez-García, Maria Rosa Domingo-Sananes, Sofia Fraile, Víctor de Lorenzo
Pubblicato in: Integr. Biol., Numero 8/4, 2016, Pagina/e 571-576, ISSN 1757-9694
Editore: Royal Society of Chemistry
DOI: 10.1039/C5IB00310E

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

Autori: Pablo I. Nikel, Danilo Pérez-Pantoja, Víctor de Lorenzo
Pubblicato in: Environmental Microbiology, Numero 18/10, 2016, Pagina/e 3565-3582, ISSN 1462-2912
Editore: 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

Autori: Juhyun Kim, Danilo Pérez-Pantoja, Rafael Silva-Rocha, Juan Carlos Oliveros, Víctor de Lorenzo
Pubblicato in: Environmental Microbiology, Numero 18/10, 2016, Pagina/e 3327-3341, ISSN 1462-2912
Editore: Blackwell Publishing Inc.
DOI: 10.1111/1462-2920.13054

Physical Forces Shape Group Identity of Swimming Pseudomonas putida Cells

Autori: David R. Espeso, Esteban Martínez-García, Víctor de Lorenzo, Ángel Goñi-Moreno
Pubblicato in: Frontiers in Microbiology, Numero 7, 2016, ISSN 1664-302X
Editore: Frontiers Media
DOI: 10.3389/fmicb.2016.01437

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

Autori: Víctor de Lorenzo, Philippe Marlière, Ricard Solé
Pubblicato in: Microbial Biotechnology, Numero 9/5, 2016, Pagina/e 618-625, ISSN 1751-7915
Editore: Microb Biotechnol.
DOI: 10.1111/1751-7915.12399

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

Autori: Ilaria Benedetti, Víctor de Lorenzo, Pablo I. Nikel
Pubblicato in: Metabolic Engineering, Numero 33, 2016, Pagina/e 109-118, ISSN 1096-7176
Editore: 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

Autori: Alejandro Arce-Rodríguez, Belén Calles, Pablo I. Nikel, Víctor de Lorenzo
Pubblicato in: Environmental Microbiology, Numero 18/10, 2016, Pagina/e 3309-3326, ISSN 1462-2912
Editore: Blackwell Publishing Inc.
DOI: 10.1111/1462-2920.13052

The quest for the minimal bacterial genome

Autori: Esteban Martínez-García, Víctor de Lorenzo
Pubblicato in: Current Opinion in Biotechnology, Numero 42, 2016, Pagina/e 216-224, ISSN 0958-1669
Editore: Elsevier BV
DOI: 10.1016/j.copbio.2016.09.001

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

Autori: Markus Schmidt, Víctor de Lorenzo
Pubblicato in: Current Opinion in Biotechnology, Numero 38, 2016, Pagina/e 90-96, ISSN 0958-1669
Editore: 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

Autori: Tomás Aparicio, Sheila I. Jensen, Alex T. Nielsen, Victor de Lorenzo, Esteban Martínez-García
Pubblicato in: Biotechnology Journal, Numero 11/10, 2016, Pagina/e 1309-1319, ISSN 1860-6768
Editore: Wiley - VCH Verlag GmbH & CO. KGaA
DOI: 10.1002/biot.201600317

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

Autori: Raúl Guantes, Ilaria Benedetti, Rafael Silva-Rocha, Víctor de Lorenzo
Pubblicato in: The ISME Journal, Numero 10/5, 2015, Pagina/e 1122-1133, ISSN 1751-7362
Editore: Nature Publishing Group
DOI: 10.1038/ismej.2015.193

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

Autori: Ilaria Benedetti, Pablo I. Nikel, Víctor de Lorenzo
Pubblicato in: Data in Brief, Numero 6, 2016, Pagina/e 738-744, ISSN 2352-3409
Editore: Elsevier BV
DOI: 10.1016/j.dib.2016.01.022

Asymmetric Enzymatic Hydration of Unactivated, Aliphatic Alkenes

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

Pseudomonas putida KT 2440 is HV 1 certified, not GRAS

Autori: Linde F. C. Kampers, Rita J. M. Volkers, Vitor A. P. Martins dos Santos
Pubblicato in: Microbial Biotechnology, 2019, ISSN 1751-7915
Editore: wiley
DOI: 10.1111/1751-7915.13443

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

Autori: Nhung Pham, Ruben van Heck, Jesse van Dam, Peter Schaap, Edoardo Saccenti, Maria Suarez-Diez
Pubblicato in: Metabolites, Numero 9/2, 2019, Pagina/e 28, ISSN 2218-1989
Editore: MDPI
DOI: 10.3390/metabo9020028

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

Autori: 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
Pubblicato in: Microbial Cell Factories, Numero 18/1, 2019, ISSN 1475-2859
Editore: 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

Autori: Sanjeevan Jahagirdar, Maria Suarez-Diez, Edoardo Saccenti
Pubblicato in: Journal of Proteome Research, Numero 18/3, 2019, Pagina/e 1099-1113, ISSN 1535-3893
Editore: American Chemical Society
DOI: 10.1021/acs.jproteome.8b00781

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

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

SyNDI: synchronous network data integration framework

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

Structural and functional insights into asymmetric enzymatic dehydration of alkenols

Autori: 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
Pubblicato in: Nature Chemical Biology, Numero 13/3, 2017, Pagina/e 275-281, ISSN 1552-4450
Editore: 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

Autori: Rebecca M. Demming, Konrad B. Otte, Bettina M. Nestl, Bernhard Hauer
Pubblicato in: ChemCatChem, Numero 9/5, 2017, Pagina/e 758-766, ISSN 1867-3880
Editore: 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)

Autori: Rebecca M. Demming, Konrad B. Otte, Bettina M. Nestl, Bernhard Hauer
Pubblicato in: ChemCatChem, Numero 9/5, 2017, Pagina/e 716-716, ISSN 1867-3880
Editore: Wiley - VCH Verlag GmbH & CO. KGaA
DOI: 10.1002/cctc.201700258

Book chapters (4)

Introduction to Genetic, Genomic and System Analyses of Pure Cultures

Autori: Víctor de Lorenzo
Pubblicato in: Hydrocarbon and Lipid Microbiology Protocols, 2017, Pagina/e 1-7, ISBN 978-3-662-50435-2
Editore: Springer Berlin Heidelberg
DOI: 10.1007/8623_2016_192

Systems and Synthetic Biology in Hydrocarbon Microbiology: Tools

Autori: Víctor de Lorenzo
Pubblicato in: Hydrocarbon and Lipid Microbiology Protocols, 2016, Pagina/e 1-7, ISBN 978-3-662-50432-1
Editore: Springer Berlin Heidelberg
DOI: 10.1007/8623_2015_185

Engineering Gram-Negative Microbial Cell Factories Using Transposon Vectors

Autori: Esteban Martínez-García, Tomás Aparicio, Víctor de Lorenzo, Pablo I. Nikel
Pubblicato in: In Vitro Mutagenesis, 2017, Pagina/e 273-293, ISBN 978-1-4939-6472-7
Editore: 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

Autori: Belén Calles, Víctor de Lorenzo
Pubblicato in: Hydrocarbon and Lipid Microbiology Protocols, 2017, Pagina/e 71-85, ISBN 978-3-662-50435-2
Editore: Springer Berlin Heidelberg
DOI: 10.1007/8623_2015_114

Thesis and dissertations (1)

Metabolic modeling to understand and redesign microbial systems

Autori: Ruben van Heck
Pubblicato in: Thesis, 2017, ISBN 9789-463434553
Editore: Wageningen University & Research