Synthetic bacterial lipid rafts to optimize industrial bioprocesses

Informations projet

Rafts4Biotech

N° de convention de subvention: 720776

DOI

10.3030/720776

Projet clôturé

Date de signature de la CE 14 Novembre 2016

Date de début 1 Janvier 2017

Date de fin 30 Juin 2021

Financé au titre de

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

Coût total

€ 6 733 580,00

Contribution de l’UE

€ 6 733 580,00

Coordonné par

AGENCIA ESTATAL CONSEJO SUPERIOR DE INVESTIGACIONES CIENTIFICAS
Spain

CORDIS fournit des liens vers les livrables publics et les publications des projets HORIZON.

Les liens vers les livrables et les publications des projets du 7e PC, ainsi que les liens vers certains types de résultats spécifiques tels que les jeux de données et les logiciels, sont récupérés dynamiquement sur OpenAIRE .

Livrables

Websites, patent fillings, videos etc. (9)

Initial communication material

A report describing the status of the first delivery of activities regarding communication and the potential impact of the stakeholders

Study cases promotional material

Delivery of communication material dedicated to promote the showcases of Rafts4Biotech among the stakeholders

Visual identity, website and social networks

Generation of a corporative logo and corporative colors for rafts4Biotech Visual identityCreation and launching of a websiteIntegration of rafts4biotech in social networks

Completion of industry events

A report of the completion of the industry event and study the possibility to interact and to partner with the companies involved in the event

Impact report

A report of the impact of the communication activities on the stakeholders and evaluation of the feedback of the stakeholders regarding the rafts4biotech activities and technology

Project management guideline meeting for project overall and WPs

Description of the agenda for Project managementGuideline meeting for project overall and completion of the work packages associated with this project

Student training activities

A report of the overall training activities that have been performed during the completion of rafts4Biotech to train the students involved in the completion of this project for their capacity to become future investigators

Final video

Video dedicated to show the execution of the overall project and the potential aspects four technology to the society and the stakeholders

Mid-project communication and engagement material

A report describing the status of the midproject delivery of activities regarding communication and engagement material and the potential impact of the stakeholders

Documents, reports (3)

Description on suitability of 2ndLMCs for industrial implementation

a report of the genetic and physiological characteristics of the second line of microbial chassis and its suitability for industrial implementation

Description of the academic and industrial dissemination activities

A report of the description of the most relevant academic and industrial dissemination activities that have been performed during the completion of this project

Impact of showcases in their respective market segments, potential to expand the technology to other market segments

A study of the Impact of the showcases in their respective market segments and description of the possibilities to integrate our raftbased technology to other market segments

Other (5)

Iterative loop 1

A report of the activities performed using the first line of microbial chassis to adapt these strains and optimise them to industrially relevant scenarios

Description of the optimal design of the microfluidic chip and the related software for transforming chip data into kinetic values

A report of the perform of the microfluidic chip and the related software for transforming chip data into kinetic values

Description of the optimization of pathways during escalation to industrial settings

A report of the mathematical calculations and in vitro experimental setup to define the suitability of the optimization of showcase pathways during escalation to industrial application

Description of the design of capillary microfluidic device and related software for automated control of bioreactor device

A report of the design of capillary microfluidic device description of the related software and the possibilities to elevate them to marketable applications

Iterative loop 2

A report of the modifications and adaptations of the synthetic lipid rafts in the second generation of microbial chassis to improve their performance in laboratory conditions

Demonstrators, pilots, prototypes (6)

Metabolomic data analyses

A report of the results and data analysis of the metabolomic data of the first and second line of microbial chassis

Presentation of Data Management Plan

A report of the main activities delineated to handle the scientific data produced during the completion of rafts4Biotech

Transcriptomics data analyses and comparison studies

A report of the results and data analysis of the transcriptomics data of the first and second line of microbial chassis

Proteomic data analyses and comparison studies

A report of the results and data analysis of the proteomics data of the first and second line of microbial chassis

2ndLMCs for Cosmetics-SC

A report of the genetic and physiological characteristics of the second line of microbial chassis that will be generated to produce the showcase CosmeticsSC

2ndLMCs for Feed-SC

A report of the genetic and physiological characteristics of the second line of microbial chassis that will be generated to produce the showcase FeedSC

Publications

Peer reviewed articles (28)

Complete Genome Sequence of the Prototrophic Bacillus subtilis subsp. subtilis Strain SP1

Auteurs: Björn Richts, Robert Hertel, Sébastien Potot, Anja Poehlein, Rolf Daniel, Ghislain Schyns, Zoltán Prágai, Fabian M. Commichau
Publié dans: Microbiology Resource Announcements, Numéro 9/32, 2020, ISSN 2576-098X
Éditeur: American Society of Microbiology
DOI: 10.1128/mra.00825-20

Engineering enzyme access tunnels

Auteurs: Piia Kokkonen, David Bednar, Gaspar Pinto, Zbynek Prokop, Jiri Damborsky
Publié dans: Biotechnology Advances, Numéro 37/6, 2019, Page(s) 107386, ISSN 0734-9750
Éditeur: Elsevier BV
DOI: 10.1016/j.biotechadv.2019.04.008

A Haloalkane Dehalogenase from Saccharomonospora viridis Strain DSM 43017, a Compost Bacterium with Unusual Catalytic Residues, Unique ( S )-Enantiopreference, and High Thermostability

Auteurs: Klaudia Chmelova, Eva Sebestova, Veronika Liskova, Andy Beier, David Bednar, Zbynek Prokop, Radka Chaloupkova, Jiri Damborsky
Publié dans: Applied and Environmental Microbiology, Numéro 86/17, 2020, ISSN 0099-2240
Éditeur: American Society for Microbiology
DOI: 10.1128/aem.02820-19

The impact of tunnel mutations on enzymatic catalysis depends on the tunnel-substrate complementarity and the rate-limiting step

Auteurs: Piia Kokkonen, Michaela Slanska, Veronika Dockalova, Gaspar P. Pinto, Esther M. Sánchez-Carnerero, Jiri Damborsky, Petr Klán, Zbynek Prokop, David Bednar
Publié dans: Computational and Structural Biotechnology Journal, Numéro 18, 2020, Page(s) 805-813, ISSN 2001-0370
Éditeur: Elsevier
DOI: 10.1016/j.csbj.2020.03.017

Structures of hyperstable ancestral haloalkane dehalogenases show restricted conformational dynamics

Auteurs: Petra Babkova, Zuzana Dunajova, Radka Chaloupkova, Jiri Damborsky, David Bednar, Martin Marek
Publié dans: Computational and Structural Biotechnology Journal, Numéro 18, 2020, Page(s) 1497-1508, ISSN 2001-0370
Éditeur: Elsevier
DOI: 10.1016/j.csbj.2020.06.021

EnzymeMiner: automated mining of soluble enzymes with diverse structures, catalytic properties and stabilities

Auteurs: Jiri Hon, Simeon Borko, Jan Stourac, Zbynek Prokop, Jaroslav Zendulka, David Bednar, Tomas Martinek, Jiri Damborsky
Publié dans: Nucleic Acids Research, Numéro 48/W1, 2020, Page(s) W104-W109, ISSN 0305-1048
Éditeur: Oxford University Press
DOI: 10.1093/nar/gkaa372

Fast Screening of Inhibitor Binding/Unbinding Using Novel Software Tool CaverDock

Auteurs: Gaspar P. Pinto, Ondrej Vavra, Jiri Filipovic, Jan Stourac, David Bednar, Jiri Damborsky
Publié dans: Frontiers in Chemistry, Numéro 7, 2019, ISSN 2296-2646
Éditeur: Frontiers
DOI: 10.3389/fchem.2019.00709

Functional redundancy and specialization of the conserved cold shock proteins in Bacillus subtilis

Auteurs: Faßhauer, Patrick; Busche, Tobias; Kalinowski, Jörn; Mäder, Ulrike; Poehlein, Anja; Daniel, Rolf; Stülke, Jörg
Publié dans: Microorganisms, Numéro 5, 2021, ISSN 2076-2607
Éditeur: MDPI
DOI: 10.5281/zenodo.4897660

Mini Bacillus PG10 as a Convenient and Effective Production Host for Lantibiotics

Auteurs: Amanda Y. van Tilburg, Auke J. van Heel, Jörg Stülke, Niels A. W. de Kok, Anne-Stéphanie Rueff, Oscar P. Kuipers
Publié dans: ACS Synthetic Biology, Numéro 9/7, 2020, Page(s) 1833-1842, ISSN 2161-5063
Éditeur: American Chemical Society
DOI: 10.1021/acssynbio.0c00194

FireProtASR: A Web Server for Fully Automated Ancestral Sequence Reconstruction

Auteurs: Milos Musil, Rayyan Tariq Khan, Andy Beier, Jan Stourac, Hannes Konegger, Jiri Damborsky, David Bednar
Publié dans: Briefings in Bioinformatics, Numéro 22/4, 2021, ISSN 1467-5463
Éditeur: Oxford University Press
DOI: 10.1093/bib/bbaa337

Fluorescent substrates for haloalkane dehalogenases: Novel probes for mechanistic studies and protein labeling

Auteurs: Veronika Dockalova, Esther M. Sanchez-Carnerero, Zuzana Dunajova, Eduardo Palao, Michaela Slanska, Tomas Buryska, Jiri Damborsky, Petr Klán, Zbynek Prokop
Publié dans: Computational and Structural Biotechnology Journal, Numéro 18, 2020, Page(s) 922-932, ISSN 2001-0370
Éditeur: Elsevier
DOI: 10.1016/j.csbj.2020.03.029

Tunable expression rate control of a growth-decoupled T7 expression system by l-arabinose only

Auteurs: Patrick Stargardt, Gerald Striedner, Juergen Mairhofer
Publié dans: Microbial Cell Factories, Numéro 20/1, 2021, ISSN 1475-2859
Éditeur: BioMed Central
DOI: 10.1186/s12934-021-01512-7

Machine Learning in Enzyme Engineering

Auteurs: Stanislav Mazurenko, Zbynek Prokop, Jiri Damborsky
Publié dans: ACS Catalysis, Numéro 10/2, 2020, Page(s) 1210-1223, ISSN 2155-5435
Éditeur: American Chemical Society
DOI: 10.1021/acscatal.9b04321

Computational Design of Stable and Soluble Biocatalysts

Auteurs: Milos Musil, Hannes Konegger, Jiri Hon, David Bednar, Jiri Damborsky
Publié dans: ACS Catalysis, Numéro 9/2, 2018, Page(s) 1033-1054, ISSN 2155-5435
Éditeur: American Chemical Society
DOI: 10.1021/acscatal.8b03613

Unchaining mini Bacillus PG10: relief of FlgM-mediated repression of autolysin genes

Auteurs: Amanda Y. van Tilburg, Julius A. Fülleborn, Alexander Reder, Uwe Völker, Jörg Stülke, Auke J. van Heel, Oscar P. Kuipers
Publié dans: Applied and Environmental Microbiology, 2021, ISSN 0099-2240
Éditeur: American Society for Microbiology
DOI: 10.1128/aem.01123-21

The contribution of bacterial genome engineering to sustainable development

Auteurs: Daniel R. Reuß, Fabian M. Commichau, Jörg Stülke
Publié dans: Microbial Biotechnology, Numéro 10/5, 2017, Page(s) 1259-1263, ISSN 1751-7915
Éditeur: John Wiley & Sons, Inc.
DOI: 10.1111/1751-7915.12784

BAGEL4: a user-friendly web server to thoroughly mine RiPPs and bacteriocins

Auteurs: Auke J van Heel, Anne de Jong, Chunxu Song, Jakob H Viel, Jan Kok, Oscar P Kuipers
Publié dans: Nucleic Acids Research, 2018, ISSN 0305-1048
Éditeur: Oxford University Press
DOI: 10.1093/nar/gky383

HotSpot Wizard 3.0: web server for automated design of mutations and smart libraries based on sequence input information

Auteurs: Lenka Sumbalova, Jan Stourac, Tomas Martinek, David Bednar, Jiri Damborsky
Publié dans: Nucleic Acids Research, Numéro 46/W1, 2018, Page(s) W356-W362, ISSN 0305-1048
Éditeur: Oxford University Press
DOI: 10.1093/nar/gky417

CalFitter: a web server for analysis of protein thermal denaturation data

Auteurs: Stanislav Mazurenko, Jan Stourac, Antonin Kunka, Sava Nedeljković, David Bednar, Zbynek Prokop, Jiri Damborsky
Publié dans: Nucleic Acids Research, Numéro 46/W1, 2018, Page(s) W344-W349, ISSN 0305-1048
Éditeur: Oxford University Press
DOI: 10.1093/nar/gky358

Increased osmolarity in biofilm triggers RcsB-dependent lipid A palmitoylation in Escherichia coli.

Auteurs: Szczesny, M., C. Beloin and J.-M. Ghigo
Publié dans: mBio. In press., 2018, ISSN 0305-1048
Éditeur: Oxford University Press
DOI: 10.1128/mBio.01415-18

Quasi-essentiality of RNase Y in Bacillus subtilis is caused by its critical role in the control of mRNA homeostasis

Auteurs: Martin Benda, Simon Woelfel, Patrick Faßhauer, Katrin Gunka, Stefan Klumpp, Anja Poehlein, Debora Kálalová, Hana Šanderová, Rolf Daniel, Libor Krásný, Jörg Stülke
Publié dans: Nucleic Acids Research, Numéro 49/12, 2021, Page(s) 7088-7102, ISSN 0305-1048
Éditeur: Oxford University Press
DOI: 10.1093/nar/gkab528

Resistance to serine in Bacillus subtilis: Identification of the serine transporter YbeC and of a metabolic network that links serine and threonine metabolism

Auteurs: Anika Klewing; Byoung-Mo Koo; Larissa Krüger; Anja Poehlein; Daniel R. Reuß; Rolf Daniel; Carol A. Gross; Jörg Stülke
Publié dans: Environmental Microbiology, Numéro 13, 2021, ISSN 1462-2920
Éditeur: Wiley
DOI: 10.1101/2020.05.20.106443

Decoding the intricate network of molecular interactions of a hyperstable engineered biocatalyst

Auteurs: Klara Markova, Klaudia Chmelova, Sérgio M. Marques, Philippe Carpentier, David Bednar, Jiri Damborsky, Martin Marek
Publié dans: Chemical Science, Numéro 11/41, 2020, Page(s) 11162-11178, ISSN 2041-6520
Éditeur: Royal Society of Chemistry
DOI: 10.1039/d0sc03367g

Subcellular Localization and Assembly Process of the Nisin Biosynthesis Machinery in Lactococcus lactis

Auteurs: Jingqi Chen, Auke J. van Heel, Oscar P. Kuipers
Publié dans: mBio, Numéro 11/6, 2020, ISSN 2161-2129
Éditeur: American Society for Microbiology
DOI: 10.1128/mbio.02825-20

Computational Modelling of Metabolic Burden and Substrate Toxicity in Escherichia coli Carrying a Synthetic Metabolic Pathway

Auteurs: Martin Demko, Lukáš Chrást, Pavel Dvořák, Jiří Damborský, David Šafránek
Publié dans: Microorganisms, Numéro 7/11, 2019, Page(s) 553, ISSN 2076-2607
Éditeur: MDPI
DOI: 10.3390/microorganisms7110553

Structural and catalytic effects of surface loop-helix transplantation within haloalkane dehalogenase family

Auteurs: Martin Marek, Radka Chaloupkova, Tatyana Prudnikova, Yukari Sato, Pavlina Rezacova, Yuji Nagata, Ivana Kuta Smatanova, Jiri Damborsky
Publié dans: Computational and Structural Biotechnology Journal, Numéro 18, 2020, Page(s) 1352-1362, ISSN 2001-0370
Éditeur: Elsevier
DOI: 10.1016/j.csbj.2020.05.019

Visualization and Analysis of the Dynamic Assembly of a Heterologous Lantibiotic Biosynthesis Complex in Bacillus subtilis

Auteurs: Jingqi Chen, Auke J. van Heel, Oscar P. Kuipers
Publié dans: mBio, 2021, ISSN 2150-7511
Éditeur: American Society of Microbiology
DOI: 10.1128/mbio.01219-21

A Bacillus subtilis   Δ pdxT mutant suppresses vitamin B6 limitation by acquiring mutations enhancing pdxS gene dosage and ammonium assimilation

Auteurs: Björn Richts, Sabine Lentes, Anja Poehlein, Rolf Daniel, Fabian M. Commichau
Publié dans: Environmental Microbiology Reports, Numéro 13/2, 2021, Page(s) 218-233, ISSN 1758-2229
Éditeur: Wiley-Blackwell
DOI: 10.1111/1758-2229.12936

Droits de propriété intellectuelle

Patent (1)

CONTINUOUS BIOPRODUCTION BY DECOUPLING GROWTH AND PRODUCTION

Numéro de demande/publication: 20 20087354
Date: 2020-12-20
Demandeur(s): ENGENES BIOTECH GMBH