RNA-based technologies for single-cell metabolite analysis

Informazioni relative al progetto

MetaRNA

ID dell’accordo di sovvenzione: 642738

DOI 10.3030/642738

Progetto chiuso

Data della firma CE 5 Dicembre 2014

Data di avvio 1 Gennaio 2015

Data di completamento 30 Giugno 2019

Finanziato da

• EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions

Costo totale € 3 995 643,24

Contributo UE € 3 995 643,24

Coordinato da

RIJKSUNIVERSITEIT GRONINGEN
Netherlands

Risultati finali

Documents, reports (15)

Cellular and in vivo delivery of RNA-based sensor

Protocol for efficient in vitro cellular and in vivo delivery of RNA-based sensors

First flux-sensor validated

A first flux-sensor validated

Elucidation of population wide production heterogeneity on the single cell level

Elucidation of population wide production heterogeneity on the single cell level for thiamine or coumarate cell factory on different fermentation scales

Quantitative MS and IMS

Combined MS and IMS methods to screen RNA libraries and characterize the ligand binding affinities and the induced conformational changes

Fluxes through the yeast cell cycle quantified
RNA-based metabolite sensor

RNA-based sensor for fructose-1,6-bisphosphate

Optimized RNA-based sensor

Optimized RNA-based sensors

Novel SELEX method

Novel SELEX method for identification of RNA molecules that bind to riboswitches

First flux-signaling metabolites identified

List with potential flux-signaling metabolites in yeast central metabolites

RNA-based sensor for thiamine or coumarate

RNA-based sensor for thiamine or coumarate sensing intracellular concentrations in the range 50-5000 ug/L

First aptamers identified

Aptamers identified for required metabolites

Adenoviral vectors

Adenoviral vectors that allow delivery of aptamers to mouse liver

Methodology to optimize RNA-based sensors

Description of methodologies for the computational design and directed evolution of RNA-based sensors

Characterisation of normal liver & liver tumour metabolic heterogeneity

Delivery of aptamers to mouse cancer models of liver cancer and characterization of organ and tumour metabolic heterogeneity

Secondary structure of aptamers in vivo

Secondary structure of a selected set of metabolite-sensing aptamers both in vitro and in vivo

Other (5)

Highest producing yeast strains

Selection (using RNA-based sensor) and biochemical characterization of highest producing yeast strain

Test of application of titratable RNA-based sensor

Test of application of titratable RNA-based sensor for sequential optimization of thiamine cell factory

Highest producing E.coli strains

Selection (using RNA-based sensor) and biochemical characterization of highest producing E.coli strains following combinatorial metabolic engineering

Scientific courses

Organization and attendance of scientific courses SC1-SC4 (M8,12,18,24) Lead participant:All

Transferable skills courses

Organization and attendance of courses on transferable skills TS1-TS3 (M18,24 and 30) Lead participant: All

Demonstrators, pilots, prototypes (1)

In vivo screening system

Development of screening system for the optimization of metabolite-sensing aptamers

Websites, patent fillings, videos etc. (1)

Project website

Project website online (M3)

Pubblicazioni

Peer reviewed articles (16)

Mechanistic insights into type I toxin antitoxin systems in Helicobacter pylori: the importance of mRNA folding in controlling toxin expression

Autori: Hélène Arnion, Dursun Nizam Korkut, Sara Masachis Gelo, Sandrine Chabas, Jérémy Reignier, Isabelle Iost, Fabien Darfeuille
Pubblicato in: Nucleic Acids Research, 2017, Pagina/e gkw1343, ISSN 0305-1048
Editore: Oxford University Press
DOI: 10.1093/nar/gkw1343

Tumour microenvironment factors shaping the cancer metabolism landscape

Autori: Dimitrios Anastasiou
Pubblicato in: British Journal of Cancer, Numero 116/3, 2016, Pagina/e 277-286, ISSN 0007-0920
Editore: Nature Publishing Group
DOI: 10.1038/bjc.2016.412

Using RNA as Molecular Code for Programming Cellular Function

Autori: Manish Kushwaha, William Rostain, Satya Prakash, John N. Duncan, Alfonso Jaramillo
Pubblicato in: ACS Synthetic Biology, Numero 5/8, 2016, Pagina/e 795-809, ISSN 2161-5063
Editore: American Chemical Society
DOI: 10.1021/acssynbio.5b00297

Next-level riboswitch development—implementation of Capture-SELEX facilitates identification of a new synthetic riboswitch

Autori: Adrien Boussebayle, Daniel Torka, Sandra Ollivaud, Johannes Braun, Cristina Bofill-Bosch, Max Dombrowski, Florian Groher, Kay Hamacher, Beatrix Suess
Pubblicato in: Nucleic Acids Research, Numero 47/9, 2019, Pagina/e 4883-4895, ISSN 0305-1048
Editore: Oxford University Press
DOI: 10.1093/nar/gkz216

Adaptive Laboratory Evolution of Antibiotic Resistance Using Different Selection Regimes Lead to Similar Phenotypes and Genotypes

Autori: Leonie J. Jahn, Christian Munck, Mostafa M. H. Ellabaan, Morten O. A. Sommer
Pubblicato in: Frontiers in Microbiology, Numero 8, 2017, ISSN 1664-302X
Editore: Frontiers Media
DOI: 10.3389/fmicb.2017.00816

Wiring cell growth to product formation

Autori: Josi Buerger, Luisa S. Gronenberg, Hans Jasper Genee, Morten O.A. Sommer
Pubblicato in: Current Opinion in Biotechnology, Numero 59, 2019, Pagina/e 85-92, ISSN 0958-1669
Editore: Elsevier BV
DOI: 10.1016/j.copbio.2019.02.014

Saccharomyces cerevisiae goes through distinct metabolic phases during its replicative lifespan

Autori: Simeon Leupold, Georg Hubmann, Athanasios Litsios, Anne C Meinema, Vakil Takhaveev, Alexandros Papagiannakis, Bastian Niebel, Georges Janssens, David Siegel, Matthias Heinemann
Pubblicato in: eLife, Numero 8, 2019, ISSN 2050-084X
Editore: eLife Sciences Publications
DOI: 10.7554/elife.41046

RNA polymerase III limits longevity downstream of TORC1

Autori: Danny Filer, Maximillian A. Thompson, Vakil Takhaveev, Adam J. Dobson, Ilektra Kotronaki, James W. M. Green, Matthias Heinemann, Jennifer M. A. Tullet, Nazif Alic
Pubblicato in: Nature, Numero 552/7684, 2017, Pagina/e 263-267, ISSN 0028-0836
Editore: Nature Publishing Group
DOI: 10.1038/nature25007

MCT2 mediates concentration-dependent inhibition of glutamine metabolism by MOG

Autori: Louise Fets, Paul C. Driscoll, Fiona Grimm, Aakriti Jain, Patrícia M. Nunes, Michalis Gounis, Ginevra Doglioni, George Papageorgiou, Timothy J. Ragan, Sebastien Campos, Mariana Silva dos Santos, James I. MacRae, Nicola O’Reilly, Alan J. Wright, Cyril H. Benes, Kevin D. Courtney, David House, Dimitrios Anastasiou
Pubblicato in: Nature Chemical Biology, Numero 14/11, 2018, Pagina/e 1032-1042, ISSN 1552-4450
Editore: Nature Publishing Group
DOI: 10.1038/s41589-018-0136-y

Chromosomal barcoding as a tool for multiplexed phenotypic characterization of laboratory evolved lineages

Autori: Leonie Johanna Jahn, Andreas Porse, Christian Munck, Daniel Simon, Svetlana Volkova, Morten Otto Alexander Sommer
Pubblicato in: Scientific Reports, Numero 8/1, 2018, ISSN 2045-2322
Editore: Nature Publishing Group
DOI: 10.1038/s41598-018-25201-5

Metabolic heterogeneity in clonal microbial populations

Autori: Vakil Takhaveev, Matthias Heinemann
Pubblicato in: Current Opinion in Microbiology, Numero 45, 2018, Pagina/e 30-38, ISSN 1369-5274
Editore: Elsevier BV
DOI: 10.1016/j.mib.2018.02.004

Robotic assisted generation of 2′-deoxy-2′-fluoro-modifed RNA aptamers – High performance enabling strategies in aptamer selection

Autori: Stefan Breuers, Laura Lledo Bryant, Tjasa Legen, Günter Mayer
Pubblicato in: Methods, Numero 161, 2019, Pagina/e 3-9, ISSN 1046-2023
Editore: Academic Press
DOI: 10.1016/j.ymeth.2019.05.022

Pharmacogenomics of GPCR Drug Targets

Autori: Alexander S. Hauser, Sreenivas Chavali, Ikuo Masuho, Leonie J. Jahn, Kirill A. Martemyanov, David E. Gloriam, M. Madan Babu
Pubblicato in: Cell, Numero 172/1-2, 2018, Pagina/e 41-54.e19, ISSN 0092-8674
Editore: Cell Press
DOI: 10.1016/j.cell.2017.11.033

A genetic selection reveals functional metastable structures embedded in a toxin-encoding mRNA

Autori: Sara Masachis, Nicolas J Tourasse, Claire Lays, Marion Faucher, Sandrine Chabas, Isabelle Iost, Fabien Darfeuille
Pubblicato in: eLife, Numero 8, 2019, ISSN 2050-084X
Editore: eLife Sciences Publications
DOI: 10.7554/elife.47549

Discovery and Characterization of Cas9 Inhibitors Disseminated across Seven Bacterial Phyla

Autori: Ruben V. Uribe, Eric van der Helm, Maria-Anna Misiakou, Sang-Woo Lee, Stefan Kol, Morten O.A. Sommer
Pubblicato in: Cell Host & Microbe, Numero 25/2, 2019, Pagina/e 233-241.e5, ISSN 1931-3128
Editore: Cell Press
DOI: 10.1016/j.chom.2019.01.003

Robust gene expression control in human cells with a novel universal TetR aptamer splicing module

Autori: Adam A Mol, Florian Groher, Britta Schreiber, Ciaran Rühmkorff, Beatrix Suess
Pubblicato in: Nucleic acid research, Numero Sep 2, 2019, Pagina/e gkz753, ISSN 0305-1048
Editore: Oxford University Press
DOI: 10.1093/nar/gkz753