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EmPowerPutida SIGNED

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

Total Cost €

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EC-Contrib. €

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Partnership

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 EmPowerPutida project word cloud

Explore the words cloud of the EmPowerPutida project. It provides you a very rough idea of what is the project "EmPowerPutida" about.

empowered    concerted    huge    genome    structured    engineer    thereby    factored    drawing    platform    opening    orthogonal    synthesis    machinery    butadiene    dna    attractive    bulk    atp    deploy    regulatory    specialty    circuit    model    uncoupling    door    putida    utilizing    power    capitalises    innovations    lactam    tabtoxin    butanol    endowment    overcoming    compounds    efficiency    bde    changing    versatility    szlig    encoded    generate    versatile    accessible    isobutanol    route    game    strain    market    ingredients    starkly    starting    gaseous    nature    herbicide    plug    bottlenecks    re    efficacy    uncoupled    industrially    refactoring    strains    secondary    stress    enhanced    matching    metabolite    engineering    pseudomonas    chemicals    derivatives    protection    tolerance    crop    demand    streamlined    bacterium    chassis    decoupled    loops    active    metabolic    butene    biosynthetic    glucose    lifestyle    outstanding    functions    iso   

Project "EmPowerPutida" data sheet

The following table provides information about the project.

Coordinator
WAGENINGEN UNIVERSITY 

Organization address
address: DROEVENDAALSESTEEG 4
city: WAGENINGEN
postcode: 6708 PB
website: http://www.wageningenur.nl/nl.htm

contact info
title: n.a.
name: n.a.
surname: n.a.
function: n.a.
email: n.a.
telephone: n.a.
fax: n.a.

 Coordinator Country Netherlands [NL]
 Project website http://www.empowerputida.eu
 Total cost 6˙839˙673 €
 EC max contribution 6˙020˙825 € (88%)
 Programme 1. H2020-EU.2.1.4. (INDUSTRIAL LEADERSHIP - Leadership in enabling and industrial technologies – Biotechnology)
 Code Call H2020-LEIT-BIO-2014-1
 Funding Scheme RIA
 Starting year 2015
 Duration (year-month-day) from 2015-05-01   to  2019-04-30

 Partnership

Take a look of project's partnership.

# participants  country  role  EC contrib. [€] 
1    WAGENINGEN UNIVERSITY NL (WAGENINGEN) coordinator 1˙357˙753.00
2    UNIVERSITAET STUTTGART DE (STUTTGART) participant 1˙348˙266.00
3    AGENCIA ESTATAL CONSEJO SUPERIOR DEINVESTIGACIONES CIENTIFICAS ES (MADRID) participant 721˙875.00
4    UNIVERSIDADE NOVA DE LISBOA PT (LISBOA) participant 621˙250.00
5    INGENZA LIMITED UK (ROSLIN) participant 614˙500.00
6    BASF SE DE (LUDWIGSHAFEN AM RHEIN) participant 592˙212.00
7    LIFEGLIMMER GMBH DE (BERLIN) participant 581˙750.00
8    ABENGOA RESEARCH SL ES (SEVILLA) participant 128˙217.00
9    LUCITE INTERNATIONAL UK LIMITED UK (BILLINGHAM) participant 55˙000.00
10    EIDGENOESSISCHE TECHNISCHE HOCHSCHULE ZUERICH CH (ZUERICH) participant 0.00
11    INSTITUTO DE TECNOLOGIA QUIMICA E BIOLOGICA - UNIVERSIDADE NOVA DE LISBOA PT (OEIRAS) participant 0.00

Map

 Project objective

We aim to engineer the lifestyle of Pseudomonas putida to generate a tailored, re-factored chassis with highly attractive new-to-nature properties, thereby opening the door to the production of thus far non-accessible compounds. This industrially driven project capitalises on the outstanding metabolic endowment and stress tolerance capabilities of this versatile bacterium for the production of specialty and bulk chemicals. Specifically, we will build streamlined P. putida strains with improved ATP availability utilizing this power on demand, decoupled from growth. The well-characterized, streamlined and re-factored strain platform will offer easy-to-use plug-in opportunities for novel, DNA-encoded functions under the control of orthogonal regulatory systems. To this end, we will deploy a concerted approach of genome refactoring, model-driven circuit design, implementation of ATP control loops, structured modelling and metabolic engineering. By drawing on a starkly improved, growth-uncoupled ATP-biosynthetic machinery, empowered P. putida strains will be able to produce a) n-butanol and isobutanol and their challenging gaseous derivatives 1-butene (BE) and (iso-)butadiene (BDE) using a novel, new-to-nature route starting from glucose, as well as b) new active ingredients for crop protection, such as tabtoxin, a high-value, ß-lactam-based secondary metabolite with a huge potential as a new herbicide. The game-changing innovations brought in – in particular the uncoupling of ATP-synthesis and production from growth - will provide strong versatility, enhanced efficiency and efficacy to the production processes, thereby overcoming current bottlenecks, matching market needs and fostering high-level research growth and development.

 Deliverables

List of deliverables.
SOPs Websites, patent fillings, videos etc. 2019-09-05 12:41:46
Short-chain alcohols-resistant Pseudomonas strains Demonstrators, pilots, prototypes 2019-04-25 16:30:28
Genome Edited P. Putida Demonstrators, pilots, prototypes 2019-04-25 16:30:28
Public Dialogue Websites, patent fillings, videos etc. 2019-09-05 12:41:41
(post-)Transcriptional genetic devices Demonstrators, pilots, prototypes 2019-04-25 16:30:28
sRNA regulators for post-transcriptional control Documents, reports 2019-04-25 16:30:27
Website & communication pipeline Websites, patent fillings, videos etc. 2019-04-25 16:30:27

Take a look to the deliverables list in detail:  detailed list of EmPowerPutida deliverables.

 Publications

year authors and title journal last update
List of publications.
2019 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
In silico-guided engineering of Pseudomonas putida towards growth under micro-oxic conditions
published pages: , ISSN: 1475-2859, DOI: 10.1186/s12934-019-1227-5
Microbial Cell Factories 18/1 2019-11-14
2018 Erno Lindfors, Jesse C. J. van Dam, Carolyn Ming Chi Lam, Niels A. Zondervan, Vitor A. P. Martins dos Santos, Maria Suarez-Diez
SyNDI: synchronous network data integration framework
published pages: , ISSN: 1471-2105, DOI: 10.1186/s12859-018-2426-5
BMC Bioinformatics 19/1 2019-11-14
2019 Sanjeevan Jahagirdar, Maria Suarez-Diez, Edoardo Saccenti
Simulation and Reconstruction of Metabolite–Metabolite Association Networks Using a Metabolic Dynamic Model and Correlation Based Algorithms
published pages: 1099-1113, ISSN: 1535-3893, DOI: 10.1021/acs.jproteome.8b00781
Journal of Proteome Research 18/3 2019-11-14
2019 Linde F. C. Kampers, Rita J. M. Volkers, Vitor A. P. Martins dos Santos
Pseudomonas putida KT 2440 is HV 1 certified, not GRAS
published pages: , ISSN: 1751-7915, DOI: 10.1111/1751-7915.13443
Microbial Biotechnology 2019-08-29
2019 Nhung Pham, Ruben van Heck, Jesse van Dam, Peter Schaap, Edoardo Saccenti, Maria Suarez-Diez
Consistency, Inconsistency, and Ambiguity of Metabolite Names in Biochemical Databases Used for Genome-Scale Metabolic Modelling
published pages: 28, ISSN: 2218-1989, DOI: 10.3390/metabo9020028
Metabolites 9/2 2019-08-29
2016 Jasper J. Koehorst, Edoardo Saccenti, Peter J. Schaap, Vitor A. P. Martins dos Santos, Maria Suarez-Diez
Protein domain architectures provide a fast, efficient and scalable alternative to sequence-based methods for comparative functional genomics
published pages: 1987, ISSN: 2046-1402, DOI: 10.12688/f1000research.9416.3
F1000Research 5 2019-06-04
2018 Rebecca M. Demming, Stephan C. Hammer, Bettina M. Nestl, Sebastian Gergel, Silvia Fademrecht, Jürgen Pleiss, Bernhard Hauer
Asymmetric Enzymatic Hydration of Unactivated, Aliphatic Alkenes
published pages: , ISSN: 1433-7851, DOI: 10.1002/anie.201810005
Angewandte Chemie International Edition 2019-04-25
2016 David R. Espeso, Esteban Martínez-García, Víctor de Lorenzo, Ángel Goñi-Moreno
Physical Forces Shape Group Identity of Swimming Pseudomonas putida Cells
published pages: , ISSN: 1664-302X, DOI: 10.3389/fmicb.2016.01437
Frontiers in Microbiology 7 2019-06-04
2016 Tomás Aparicio, Sheila I. Jensen, Alex T. Nielsen, Victor de Lorenzo, Esteban Martínez-García
The Ssr protein (T1E_1405) from Pseudomonas putida DOT-T1E enables oligonucleotide-based recombineering in platform strain P. putida EM42
published pages: 1309-1319, ISSN: 1860-6768, DOI: 10.1002/biot.201600317
Biotechnology Journal 11/10 2019-06-04
2016 Esteban Martínez-García, Víctor de Lorenzo
The quest for the minimal bacterial genome
published pages: 216-224, ISSN: 0958-1669, DOI: 10.1016/j.copbio.2016.09.001
Current Opinion in Biotechnology 42 2019-06-04
2016 Markus Schmidt, Víctor de Lorenzo
Synthetic bugs on the loose: containment options for deeply engineered (micro)organisms
published pages: 90-96, ISSN: 0958-1669, DOI: 10.1016/j.copbio.2016.01.006
Current Opinion in Biotechnology 38 2019-06-04
2016 Ilaria Benedetti, Pablo I. Nikel, Víctor de Lorenzo
Data on the standardization of a cyclohexanone-responsive expression system for Gram-negative bacteria
published pages: 738-744, ISSN: 2352-3409, DOI: 10.1016/j.dib.2016.01.022
Data in Brief 6 2019-06-04
2016 Pablo I. Nikel, Danilo Pérez-Pantoja, Víctor de Lorenzo
Pyridine nucleotide transhydrogenases enable redox balance of Pseudomonas putida during biodegradation of aromatic compounds
published pages: 3565-3582, ISSN: 1462-2912, DOI: 10.1111/1462-2920.13434
Environmental Microbiology 18/10 2019-06-04
2016 Aitor de las Heras, Esteban Martínez-García, Maria Rosa Domingo-Sananes, Sofia Fraile, Víctor de Lorenzo
Rationally rewiring the connectivity of the XylR/Pu regulatory node of the m-xylene degradation pathway in Pseudomonas putida
published pages: 571-576, ISSN: 1757-9694, DOI: 10.1039/C5IB00310E
Integr. Biol. 8/4 2019-06-04
2017 Rebecca M. Demming, Konrad B. Otte, Bettina M. Nestl, Bernhard Hauer
Inside Cover: Optimized Reaction Conditions Enable the Hydration of Non-natural Substrates by the Oleate Hydratase from Elizabethkingia meningoseptica (ChemCatChem 5/2017)
published pages: 716-716, ISSN: 1867-3880, DOI: 10.1002/cctc.201700258
ChemCatChem 9/5 2019-06-04
2017 Rebecca M. Demming, Konrad B. Otte, Bettina M. Nestl, Bernhard Hauer
Optimized Reaction Conditions Enable the Hydration of Non-natural Substrates by the Oleate Hydratase from Elizabethkingia meningoseptica
published pages: 758-766, ISSN: 1867-3880, DOI: 10.1002/cctc.201601329
ChemCatChem 9/5 2019-06-04
2016 Víctor de Lorenzo, Philippe Marlière, Ricard Solé
Bioremediation at a global scale: from the test tube to planet Earth
published pages: 618-625, ISSN: 1751-7915, DOI: 10.1111/1751-7915.12399
Microbial Biotechnology 9/5 2019-06-04
2017 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
Structural and functional insights into asymmetric enzymatic dehydration of alkenols
published pages: 275-281, ISSN: 1552-4450, DOI: 10.1038/nchembio.2271
Nature Chemical Biology 13/3 2019-06-04
2015 Raúl Guantes, Ilaria Benedetti, Rafael Silva-Rocha, Víctor de Lorenzo
Transcription factor levels enable metabolic diversification of single cells of environmental bacteria
published pages: 1122-1133, ISSN: 1751-7362, DOI: 10.1038/ismej.2015.193
The ISME Journal 10/5 2019-06-04
2016 Alejandro Arce-Rodríguez, Belén Calles, Pablo I. Nikel, Víctor de Lorenzo
The RNA chaperone Hfq enables the environmental stress tolerance super-phenotype of P seudomonas putida
published pages: 3309-3326, ISSN: 1462-2912, DOI: 10.1111/1462-2920.13052
Environmental Microbiology 18/10 2019-04-25
2016 Juhyun Kim, Danilo Pérez-Pantoja, Rafael Silva-Rocha, Juan Carlos Oliveros, Víctor de Lorenzo
High-resolution analysis of the m -xylene/toluene biodegradation subtranscriptome of P seudomonas putida mt-2
published pages: 3327-3341, ISSN: 1462-2912, DOI: 10.1111/1462-2920.13054
Environmental Microbiology 18/10 2019-06-04
2016 Ilaria Benedetti, Víctor de Lorenzo, Pablo I. Nikel
Genetic programming of catalytic Pseudomonas putida biofilms for boosting biodegradation of haloalkanes
published pages: 109-118, ISSN: 1096-7176, DOI: 10.1016/j.ymben.2015.11.004
Metabolic Engineering 33 2019-06-04

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