Genome-scale strain designs based on regulatory minimal cut sets.
BACKGROUND
Stoichiometric and constraint-based methods of computational strain design have become an important tool for rational metabolic engineering. One of those relies on the concept of constrained minimal cut sets (cMCSs). However, as most other techniques, cMCSs may consider only reaction (or gene) knockouts to achieve a desired phenotype.


RESULTS
We generalize the cMCSs approach to constrained regulatory MCSs (cRegMCSs), where up/downregulation of reaction rates can be combined along with reaction deletions. We show that flux up/downregulations can virtually be treated as cuts allowing their direct integration into the algorithmic framework of cMCSs. Because of vastly enlarged search spaces in genome-scale networks, we developed strategies to (optionally) preselect suitable candidates for flux regulation and novel algorithmic techniques to further enhance efficiency and speed of cMCSs calculation. We illustrate the cRegMCSs approach by a simple example network and apply it then by identifying strain designs for ethanol production in a genome-scale metabolic model of Escherichia coli. The results clearly show that cRegMCSs combining reaction deletions and flux regulations provide a much larger number of suitable strain designs, many of which are significantly smaller relative to cMCSs involving only knockouts. Furthermore, with cRegMCSs, one may also enable the fine tuning of desired behaviours in a narrower range. The new cRegMCSs approach may thus accelerate the implementation of model-based strain designs for the bio-based production of fuels and chemicals.


METHODS
MATLAB code and the examples can be downloaded at http://www.mpi-magdeburg.mpg.de/projects/cna/etcdownloads.html.


BACKGROUND
krishna.mahadevan@utoronto.ca or klamt@mpi-magdeburg.mpg.de


BACKGROUND
Supplementary data are available at Bioinformatics online.
Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5S3E5, Canada, Institute of Biomaterials and Biomedical Engineering, Toronto, ON, M5S 3G9, Canada and.
Radhakrishnan
R
Mahadevan
Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, D-39106, Germany.
Axel
A
von Kamp
Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, D-39106, Germany.
Steffen
S
Klamt
D000465:Algorithms; D003198:Computer Simulation; D004926:Escherichia coli / Q000145:classification / Q000235:genetics*; D000431:Ethanol / Q000378:metabolism*; D005818:Genetic Engineering; D016680:Genome, Bacterial; D053858:Metabolic Networks and Pathways / Q000235:genetics*; D008954:Models, Biological; D008962:Models, Theoretical; D010641:Phenotype
D000431:Ethanol