title: Genome-scale reconstruction and system level investigation of the metabolic network of Methylobacterium extorquens AM1.
abstract: BACKGROUND
  Methylotrophic microorganisms are playing a key role in biogeochemical processes - especially the global carbon cycle - and have gained interest for biotechnological purposes. Significant progress was made in the recent years in the biochemistry, genetics, genomics, and physiology of methylotrophic bacteria, showing that methylotrophy is much more widespread and versatile than initially assumed. Despite such progress, system-level description of the methylotrophic metabolism is currently lacking, and much remains to understand regarding the network-scale organization and properties of methylotrophy, and how the methylotrophic capacity emerges from this organization, especially in facultative organisms.
  
  
  RESULTS
  In this work, we report on the integrated, system-level investigation of the metabolic network of the facultative methylotroph Methylobacterium extorquens AM1, a valuable model of methylotrophic bacteria. The genome-scale metabolic network of the bacterium was reconstructed and contains 1139 reactions and 977 metabolites. The sub-network operating upon methylotrophic growth was identified from both in silico and experimental investigations, and 13C-fluxomics was applied to measure the distribution of metabolic fluxes under such conditions. The core metabolism has a highly unusual topology, in which the unique enzymes that catalyse the key steps of C1 assimilation are tightly connected by several, large metabolic cycles (serine cycle, ethylmalonyl-CoA pathway, TCA cycle, anaplerotic processes). The entire set of reactions must operate as a unique process to achieve C1 assimilation, but was shown to be structurally fragile based on network analysis. This observation suggests that in nature a strong pressure of selection must exist to maintain the methylotrophic capability. Nevertheless, substantial substrate cycling could be measured within C2/C3/C4 inter-conversions, indicating that the metabolic network is highly versatile around a flexible backbone of central reactions that allows rapid switching to multi-carbon sources.
  
  
  CONCLUSIONS
  This work emphasizes that the metabolism of M. extorquens AM1 is adapted to its lifestyle not only in terms of enzymatic equipment, but also in terms of network-level structure and regulation. It suggests that the metabolism of the bacterium has evolved both structurally and functionally to an efficient but transitory utilization of methanol. Besides, this work provides a basis for metabolic engineering to convert methanol into value-added products.
authors.affiliation: Institute of Microbiology, ETH Zürich, 8093 Zürich, Switzerland.
authors.forename: Rémi
authors.initials: R
authors.lastname: Peyraud
authors.forename: Kathrin
authors.initials: K
authors.lastname: Schneider
authors.forename: Patrick
authors.initials: P
authors.lastname: Kiefer
authors.forename: Stéphane
authors.initials: S
authors.lastname: Massou
authors.forename: Julia A
authors.initials: JA
authors.lastname: Vorholt
authors.forename: Jean-Charles
authors.initials: JC
authors.lastname: Portais
mesh_terms: D000222:Adaptation, Physiological; D016680:Genome, Bacterial; D053858:Metabolic Networks and Pathways; D020601:Methylobacterium extorquens / Q000235:genetics / Q000378:metabolism*; D008954:Models, Biological; D049490:Systems Biology
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