title: Proteomics-based metabolic modeling and characterization of the cellulolytic bacterium Thermobifida fusca.
abstract: BACKGROUND
  Thermobifida fusca is a cellulolytic bacterium with potential to be used as a platform organism for sustainable industrial production of biofuels, pharmaceutical ingredients and other bioprocesses due to its capability of potential to convert plant biomass to value-added chemicals. To best develop T. fusca as a bioprocess organism, it is important to understand its native cellular processes. In the current study, we characterize the metabolic network of T. fusca through reconstruction of a genome-scale metabolic model and proteomics data. The overall goal of this study was to use multiple metabolic models generated by different methods and comparison to experimental data to gain a high-confidence understanding of the T. fusca metabolic network.
  
  
  RESULTS
  We report the generation of three versions of a metabolic model of Thermobifida fusca sp. XY developed using three different approaches (automated, semi-automated, and proteomics-derived). The model closest to in vivo growth was the proteomics-derived model that consists of 975 reactions involving 1382 metabolites and account for 316 EC numbers (296 genes). The model was optimized for biomass production with the optimal flux of 0.48 doublings per hour when grown on cellobiose with a substrate uptake rate of 0.25 mmole/h. In vivo activity of the DXP pathway for terpenoid biosynthesis was also confirmed using real-time PCR.
  
  
  CONCLUSIONS
  iTfu296 provides a platform to understand and explore the metabolic capabilities of the actinomycete T. fusca for the potential use in bioprocess industries for the production of biofuel and pharmaceutical ingredients. By comparing different model reconstruction methods, the use of high-throughput proteomics data as a starting point proved to be the most accurate to in vivo growth.
authors.forename: Niti
authors.initials: N
authors.lastname: Vanee
authors.forename: J Paul
authors.initials: JP
authors.lastname: Brooks
authors.forename: Victor
authors.initials: V
authors.lastname: Spicer
authors.forename: Dmitriy
authors.initials: D
authors.lastname: Shamshurin
authors.forename: Oleg
authors.initials: O
authors.lastname: Krokhin
authors.forename: John A
authors.initials: JA
authors.lastname: Wilkins
authors.forename: Yu
authors.initials: Y
authors.lastname: Deng
authors.affiliation: Virginia Commonwealth University, Richmond, USA. ssfong@vcu.edu.
authors.forename: Stephen S
authors.initials: SS
authors.lastname: Fong
mesh_terms: D000192:Actinomycetales / Q000166:cytology* / Q000235:genetics / Q000378:metabolism*; D056804:Biofuels; D015964:Gene Expression Regulation, Bacterial; D053858:Metabolic Networks and Pathways; D008954:Models, Biological; D040901:Proteomics / Q000379:methods*; D013729:Terpenes / Q000378:metabolism
chemical_list: D056804:Biofuels; D013729:Terpenes