Elucidating the adaptation and temporal coordination of metabolic pathways using in-silico evolution.
Cellular metabolism, the interconversion of small molecules by chemical reactions, is a tightly coordinated process that requires integration of diverse environmental and intracellular cues. While for many organisms the topology of the network of metabolic reactions is increasingly known, the regulatory principles that shape the network's adaptation to diverse and changing environments remain largely elusive. To investigate the principles of metabolic adaptation and regulation in metabolic pathways, we propose a computational approach based on in-silico evolution. Rather than analyzing existing regulatory schemes, we let a population of minimal, prototypical metabolic cells evolve rate constants and appropriate regulatory schemes that allow for optimal growth in static and fluctuating environments. Applying our approach to a small, but already sufficiently complex, minimal system reveals intricate transitions between metabolic modes. These results have implications for trade-offs in resource allocation. Going from static to varying environments, we show that for fluctuating nutrient availability, active metabolic regulation results in a significantly increased overall rate of metabolism.
Institute for Theoretical Biology, Humboldt University of Berlin, Invalidenstrasse 43, 10115 Berlin, Germany.
Willi
W
Gottstein
Johann Radon Institute for Computational and Applied Mathematics, Austrian Academy of Sciences, Apostelgasse 23, 1030 Wien, Austria; CzechGlobe - Global Change Research Center, Academy of Sciences of the Czech Republic, Belidla 986/4a, 60300 Brno, Czech Republic.
Stefan
S
Müller
Institute for Theoretical Biology, Charite Universitätsmedizin, Invalidenstrasse 43, 10115 Berlin, Germany.
Hanspeter
H
Herzel
Institute for Theoretical Biology, Humboldt University of Berlin, Invalidenstrasse 43, 10115 Berlin, Germany; CzechGlobe - Global Change Research Center, Academy of Sciences of the Czech Republic, Belidla 986/4a, 60300 Brno, Czech Republic. Electronic address: ralf.steuer@hu-berlin.de.
Ralf
R
Steuer
D000222:Adaptation, Physiological / Q000235:genetics*; D000465:Algorithms; D000818:Animals; D001683:Biological Clocks / Q000235:genetics*; D003198:Computer Simulation; D019143:Evolution, Molecular; D006801:Humans; D064688:Metabolic Flux Analysis / Q000379:methods*; D055442:Metabolome / Q000235:genetics*; D008957:Models, Genetic; D015398:Signal Transduction / Q000235:genetics*
Evolutionary algorithms; Flux-balance analysis; Metabolic oscillations; Metabolism; Systems biology