title: Characterizing acetogenic metabolism using a genome-scale metabolic reconstruction of Clostridium ljungdahlii.
abstract: BACKGROUND
  The metabolic capabilities of acetogens to ferment a wide range of sugars, to grow autotrophically on H2/CO2, and more importantly on synthesis gas (H2/CO/CO2) make them very attractive candidates as production hosts for biofuels and biocommodities. Acetogenic metabolism is considered one of the earliest modes of bacterial metabolism. A thorough understanding of various factors governing the metabolism, in particular energy conservation mechanisms, is critical for metabolic engineering of acetogens for targeted production of desired chemicals.
  
  
  RESULTS
  Here, we present the genome-scale metabolic network of Clostridium ljungdahlii, the first such model for an acetogen. This genome-scale model (iHN637) consisting of 637 genes, 785 reactions, and 698 metabolites captures all the major central metabolic and biosynthetic pathways, in particular pathways involved in carbon fixation and energy conservation. A combination of metabolic modeling, with physiological and transcriptomic data provided insights into autotrophic metabolism as well as aided the characterization of a nitrate reduction pathway in C. ljungdahlii. Analysis of the iHN637 metabolic model revealed that flavin based electron bifurcation played a key role in energy conservation during autotrophic growth and helped identify genes for some of the critical steps in this mechanism.
  
  
  CONCLUSIONS
  iHN637 represents a predictive model that recapitulates experimental data, and provides valuable insights into the metabolic response of C. ljungdahlii to genetic perturbations under various growth conditions. Thus, the model will be instrumental in guiding metabolic engineering of C. ljungdahlii for the industrial production of biocommodities and biofuels.
authors.affiliation: Department of Bioengineering, University of California San Diego, La Jolla, CA, USA. kzengler@ucsd.edu.
authors.forename: Harish
authors.initials: H
authors.lastname: Nagarajan
authors.forename: Merve
authors.initials: M
authors.lastname: Sahin
authors.forename: Juan
authors.initials: J
authors.lastname: Nogales
authors.forename: Haythem
authors.initials: H
authors.lastname: Latif
authors.forename: Derek R
authors.initials: DR
authors.lastname: Lovley
authors.forename: Ali
authors.initials: A
authors.lastname: Ebrahim
authors.forename: Karsten
authors.initials: K
authors.lastname: Zengler
mesh_terms: D000085:Acetates / Q000378:metabolism*; D056804:Biofuels; D003013:Clostridium / Q000235:genetics* / Q000378:metabolism*; D016678:Genome; D060847:Metabolic Engineering; D053858:Metabolic Networks and Pathways / Q000235:genetics
chemical_list: D000085:Acetates; D056804:Biofuels