RNA-based technologies for single-cell metabolite analysis

Project Information

MetaRNA

Grant agreement ID: 642738

DOI

10.3030/642738

Project closed

EC signature date 5 December 2014

Start date 1 January 2015

End date 30 June 2019

Funded under

• EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions

Total cost

€ 3 995 643,24

EU contribution

€ 3 995 643,24

Coordinated by

RIJKSUNIVERSITEIT GRONINGEN
Netherlands

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Deliverables

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)

Publications

Peer reviewed articles (16)

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

Author(s): Hélène Arnion, Dursun Nizam Korkut, Sara Masachis Gelo, Sandrine Chabas, Jérémy Reignier, Isabelle Iost, Fabien Darfeuille
Published in: Nucleic Acids Research, 2017, Page(s) gkw1343, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkw1343

Tumour microenvironment factors shaping the cancer metabolism landscape

Author(s): Dimitrios Anastasiou
Published in: British Journal of Cancer, Issue 116/3, 2016, Page(s) 277-286, ISSN 0007-0920
Publisher: Nature Publishing Group
DOI: 10.1038/bjc.2016.412

Using RNA as Molecular Code for Programming Cellular Function

Author(s): Manish Kushwaha, William Rostain, Satya Prakash, John N. Duncan, Alfonso Jaramillo
Published in: ACS Synthetic Biology, Issue 5/8, 2016, Page(s) 795-809, ISSN 2161-5063
Publisher: American Chemical Society
DOI: 10.1021/acssynbio.5b00297

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

Author(s): Adrien Boussebayle, Daniel Torka, Sandra Ollivaud, Johannes Braun, Cristina Bofill-Bosch, Max Dombrowski, Florian Groher, Kay Hamacher, Beatrix Suess
Published in: Nucleic Acids Research, Issue 47/9, 2019, Page(s) 4883-4895, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkz216

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

Author(s): Leonie J. Jahn, Christian Munck, Mostafa M. H. Ellabaan, Morten O. A. Sommer
Published in: Frontiers in Microbiology, Issue 8, 2017, ISSN 1664-302X
Publisher: Frontiers Media
DOI: 10.3389/fmicb.2017.00816

Wiring cell growth to product formation

Author(s): Josi Buerger, Luisa S. Gronenberg, Hans Jasper Genee, Morten O.A. Sommer
Published in: Current Opinion in Biotechnology, Issue 59, 2019, Page(s) 85-92, ISSN 0958-1669
Publisher: Elsevier BV
DOI: 10.1016/j.copbio.2019.02.014

Saccharomyces cerevisiae goes through distinct metabolic phases during its replicative lifespan

Author(s): Simeon Leupold, Georg Hubmann, Athanasios Litsios, Anne C Meinema, Vakil Takhaveev, Alexandros Papagiannakis, Bastian Niebel, Georges Janssens, David Siegel, Matthias Heinemann
Published in: eLife, Issue 8, 2019, ISSN 2050-084X
Publisher: eLife Sciences Publications
DOI: 10.7554/elife.41046

RNA polymerase III limits longevity downstream of TORC1

Author(s): Danny Filer, Maximillian A. Thompson, Vakil Takhaveev, Adam J. Dobson, Ilektra Kotronaki, James W. M. Green, Matthias Heinemann, Jennifer M. A. Tullet, Nazif Alic
Published in: Nature, Issue 552/7684, 2017, Page(s) 263-267, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/nature25007

MCT2 mediates concentration-dependent inhibition of glutamine metabolism by MOG

Author(s): 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
Published in: Nature Chemical Biology, Issue 14/11, 2018, Page(s) 1032-1042, ISSN 1552-4450
Publisher: Nature Publishing Group
DOI: 10.1038/s41589-018-0136-y

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

Author(s): Leonie Johanna Jahn, Andreas Porse, Christian Munck, Daniel Simon, Svetlana Volkova, Morten Otto Alexander Sommer
Published in: Scientific Reports, Issue 8/1, 2018, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-018-25201-5

Metabolic heterogeneity in clonal microbial populations

Author(s): Vakil Takhaveev, Matthias Heinemann
Published in: Current Opinion in Microbiology, Issue 45, 2018, Page(s) 30-38, ISSN 1369-5274
Publisher: 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

Author(s): Stefan Breuers, Laura Lledo Bryant, Tjasa Legen, Günter Mayer
Published in: Methods, Issue 161, 2019, Page(s) 3-9, ISSN 1046-2023
Publisher: Academic Press
DOI: 10.1016/j.ymeth.2019.05.022

Pharmacogenomics of GPCR Drug Targets

Author(s): Alexander S. Hauser, Sreenivas Chavali, Ikuo Masuho, Leonie J. Jahn, Kirill A. Martemyanov, David E. Gloriam, M. Madan Babu
Published in: Cell, Issue 172/1-2, 2018, Page(s) 41-54.e19, ISSN 0092-8674
Publisher: Cell Press
DOI: 10.1016/j.cell.2017.11.033

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

Author(s): Sara Masachis, Nicolas J Tourasse, Claire Lays, Marion Faucher, Sandrine Chabas, Isabelle Iost, Fabien Darfeuille
Published in: eLife, Issue 8, 2019, ISSN 2050-084X
Publisher: eLife Sciences Publications
DOI: 10.7554/elife.47549

Discovery and Characterization of Cas9 Inhibitors Disseminated across Seven Bacterial Phyla

Author(s): Ruben V. Uribe, Eric van der Helm, Maria-Anna Misiakou, Sang-Woo Lee, Stefan Kol, Morten O.A. Sommer
Published in: Cell Host & Microbe, Issue 25/2, 2019, Page(s) 233-241.e5, ISSN 1931-3128
Publisher: 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

Author(s): Adam A Mol, Florian Groher, Britta Schreiber, Ciaran Rühmkorff, Beatrix Suess
Published in: Nucleic acid research, Issue Sep 2, 2019, Page(s) gkz753, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkz753