Enforced ATP wasting as a general design principle to rationally engineer microbial cell factories

Project Information

StrainBooster

Grant agreement ID: 721176

DOI

10.3030/721176

Project closed

EC signature date 20 February 2017

Start date 1 May 2017

End date 31 December 2022

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 1 998 750,00

EU contribution

€ 1 998 750,00

Coordinated by

MAX-PLANCK-GESELLSCHAFT ZUR FORDERUNG DER WISSENSCHAFTEN EV
Germany

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 .

Publications

Peer reviewed articles (21)

Analyzing and Resolving Infeasibility in Flux Balance Analysis of Metabolic Networks

Author(s): Steffen Klamt; Axel von Kamp
Published in: Metabolites, Issue 22181989, 2022, Page(s) 585, ISSN 2218-1989
Publisher: MDPI
DOI: 10.3390/metabo12070585

StrainDesign: a comprehensive Python package for computational design of metabolic networks

Author(s): Philipp Schneider; Pavlos Stephanos Bekiaris; Axel von Kamp; Steffen Klamt
Published in: Bioinformatics, Issue 13674803, 2022, Page(s) 4981–4983, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btac632

An extended and generalized framework for the calculation of metabolic intervention strategies based on minimal cut sets

Author(s): Philipp Schneider, Axel von Kamp, Steffen Klamt
Published in: PLOS Computational Biology, Issue 16/7, 2020, Page(s) e1008110, ISSN 1553-7358
Publisher: Public Library of Science
DOI: 10.1371/journal.pcbi.1008110

CNApy: a CellNetAnalyzer GUI in Python for analyzing and designing metabolic networks

Author(s): Sven Thiele; Axel von Kamp; Pavlos Stephanos Bekiaris; Philipp Schneider; Steffen Klamt
Published in: Bioinformatics, Issue 38, 2022, Page(s) 1467-1469, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btab828

Automatic construction of metabolic models with enzyme constraints

Author(s): Bekiaris, Pavlos Stephanos; Klamt, Steffen
Published in: BMC Bioinformatics, Issue 21, 2020, Page(s) 19, ISSN 1471-2105
Publisher: BioMed Central
DOI: 10.1186/s12859-019-3329-9

Speeding up the core algorithm for the dual calculation of minimal cut sets in large metabolic networks

Author(s): Steffen Klamt; Radhakrishnan Mahadevan; Axel von Kamp
Published in: BMC Bioinformatics, Issue 21, 2020, Page(s) 510, ISSN 1471-2105
Publisher: BioMed Central
DOI: 10.1186/s12859-020-03837-3

Enabling anaerobic growth of Escherichia coli on glycerol in defined minimal medium using acetate as redox sink

Author(s): Simon Boecker; Sebastián Espinel-Ríos; Katja Bettenbrock; Steffen Klamt
Published in: Metabolic Engineering, Issue 73, 2022, Page(s) 50-57, ISSN 1096-7176
Publisher: Academic Press
DOI: 10.1016/j.ymben.2022.05.006

Maximizing batch fermentation efficiency by constrained model‐based optimization and predictive control of adenosine triphosphate turnover

Author(s): Sebastián Espinel Ríos; Katja Bettenbrock; Steffen Klamt; Rolf Findeisen
Published in: AIChE-Journal, Issue 68, 2022, Page(s) e17555, ISSN 1547-5905
Publisher: American Institute of Chemical Engineers
DOI: 10.1002/aic.17555

Deciphering the physiological response of Escherichia coli under high ATP demand

Author(s): Simon Boecker; Giulia Slaviero; Thorben Schramm; Witold Szymanski; Ralf Steuer; Hannes Link; Steffen Klamt
Published in: Molecular Systems Biology, Issue 17, 2021, Page(s) e10504, ISSN 1744-4292
Publisher: Nature Publishing Group
DOI: 10.15252/msb.202110504

Temperature-dependent dynamic control of the TCA cycle increases volumetric productivity of itaconic acid production by Escherichia coli

Author(s): Björn-Johannes Harder, Katja Bettenbrock, Steffen Klamt
Published in: Biotechnology and Bioengineering, Issue 115/1, 2018, Page(s) 156-164, ISSN 0006-3592
Publisher: Wiley - V C H Verlag GmbbH & Co.
DOI: 10.1002/bit.26446

When Do Two-Stage Processes Outperform One-Stage Processes?

Author(s): Steffen Klamt, Radhakrishnan Mahadevan, Oliver Hädicke
Published in: Biotechnology Journal, Issue 13/2, 2018, Page(s) 1700539, ISSN 1860-6768
Publisher: Wiley - VCH Verlag GmbH & CO. KGaA
DOI: 10.1002/biot.201700539

Growth-coupled overproduction is feasible for almost all metabolites in five major production organisms

Author(s): Axel von Kamp, Steffen Klamt
Published in: Nature Communications, Issue 8, 2017, Page(s) 15956, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/ncomms15956

A mathematical framework for yield ( vs. rate) optimization in constraint-based modeling and applications in metabolic engineering

Author(s): Steffen Klamt, Stefan Müller, Georg Regensburger, Jürgen Zanghellini
Published in: Metabolic Engineering, Issue 47, 2018, Page(s) 153-169, ISSN 1096-7176
Publisher: Academic Press
DOI: 10.1016/j.ymben.2018.02.001

Use of CellNetAnalyzer in biotechnology and metabolic engineering

Author(s): Axel von Kamp, Sven Thiele, Oliver Hädicke, Steffen Klamt
Published in: Journal of Biotechnology, Issue 261, 2017, Page(s) 221-228, ISSN 0168-1656
Publisher: Elsevier BV
DOI: 10.1016/j.jbiotec.2017.05.001

OptMDFpathway: Identification of metabolic pathways with maximal thermodynamic driving force and its application for analyzing the endogenous CO2 fixation potential of Escherichia coli

Author(s): Oliver Hädicke, Axel von Kamp, Timur Aydogan, Steffen Klamt
Published in: PLOS Computational Biology, Issue 14/9, 2018, Page(s) e1006492, ISSN 1553-7358
Publisher: PLOS
DOI: 10.1371/journal.pcbi.1006492

Broadening the Scope of Enforced ATP Wasting as a Tool for Metabolic Engineering in Escherichia coli

Author(s): Simon Boecker, Ahmed Zahoor, Thorben Schramm, Hannes Link, Steffen Klamt
Published in: Biotechnology Journal, Issue 14/9, 2019, Page(s) 1800438, ISSN 1860-6768
Publisher: Wiley - VCH Verlag GmbH & CO. KGaA
DOI: 10.1002/biot.201800438

Characterizing and ranking computed metabolic engineering strategies

Author(s): Philipp Schneider, Steffen Klamt
Published in: Bioinformatics, Issue 35/17, 2019, Page(s) 3063-3072, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/bty1065

MoVE identifies metabolic valves to switch between phenotypic states

Author(s): Naveen Venayak, Axel von Kamp, Steffen Klamt, Radhakrishnan Mahadevan
Published in: Nature Communications, Issue 9/1, 2018, Page(s) 5332, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-018-07719-4

Systematizing the different notions of growth-coupled product synthesis and a single framework for computing corresponding strain designs.

Author(s): Philipp Schneider; Radhakrishnan Mahadevan; Steffen Klamt
Published in: Biotechnology Journal, Issue 16, 2021, Page(s) e2100236, ISSN 1860-7314
Publisher: Wiley-VCH GmbH
DOI: 10.1002/biot.202100236

Increasing ATP turnover boosts productivity of 2,3-butanediol synthesis in Escherichia coli

Author(s): Simon Boecker; Björn-Johannes Harder; Regina Kutscha; Stefan Pflügl; Steffen Klamt
Published in: Microbial Cell Factories, Issue 20, 2021, Page(s) 63, ISSN 1475-2859
Publisher: BioMed Central
DOI: 10.1186/s12934-021-01554-x

ATPase-based implementation of enforced ATP wasting in Saccharomyces cerevisiae for improved ethanol production

Author(s): Ahmed Zahoor, Katrin Messerschmidt, Simon Boecker, Steffen Klamt
Published in: Biotechnology for Biofuels, Issue 13/1, 2020, ISSN 1754-6834
Publisher: BioMed Central
DOI: 10.1186/s13068-020-01822-9