Deliverables
Protocol for efficient in vitro cellular and in vivo delivery of RNA-based sensors
First flux-sensor validatedA first flux-sensor validated
Elucidation of population wide production heterogeneity on the single cell levelElucidation of population wide production heterogeneity on the single cell level for thiamine or coumarate cell factory on different fermentation scales
Quantitative MS and IMSCombined 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 quantifiedRNA-based metabolite sensor
RNA-based sensor for fructose-1,6-bisphosphate
Optimized RNA-based sensorOptimized RNA-based sensors
Novel SELEX methodNovel SELEX method for identification of RNA molecules that bind to riboswitches
First flux-signaling metabolites identifiedList with potential flux-signaling metabolites in yeast central metabolites
RNA-based sensor for thiamine or coumarateRNA-based sensor for thiamine or coumarate sensing intracellular concentrations in the range 50-5000 ug/L
First aptamers identifiedAptamers identified for required metabolites
Adenoviral vectorsAdenoviral vectors that allow delivery of aptamers to mouse liver
Methodology to optimize RNA-based sensorsDescription of methodologies for the computational design and directed evolution of RNA-based sensors
Characterisation of normal liver & liver tumour metabolic heterogeneityDelivery of aptamers to mouse cancer models of liver cancer and characterization of organ and tumour metabolic heterogeneity
Secondary structure of aptamers in vivoSecondary structure of a selected set of metabolite-sensing aptamers both in vitro and in vivo
Selection (using RNA-based sensor) and biochemical characterization of highest producing yeast strain
Test of application of titratable RNA-based sensorTest of application of titratable RNA-based sensor for sequential optimization of thiamine cell factory
Highest producing E.coli strainsSelection (using RNA-based sensor) and biochemical characterization of highest producing E.coli strains following combinatorial metabolic engineering
Scientific coursesOrganization and attendance of scientific courses SC1-SC4 (M8,12,18,24) Lead participant:All
Transferable skills coursesOrganization and attendance of courses on transferable skills TS1-TS3 (M18,24 and 30) Lead participant: All
Development of screening system for the optimization of metabolite-sensing aptamers
Project website online (M3)
Publications
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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