title: In Silico Metabolic Model and Protein Expression of Haemophilus influenzae Strain Rd KW20 in Rich Medium.
abstract: The intermediary metabolism of Haemophilus influenzae strain Rd KW20 was studied by a combination of protein expression analysis using a recently developed direct proteomics approach, mutational analysis, and mathematical modeling. Special emphasis was placed on carbon utilization, sugar fermentation, TCA cycle, and electron transport of H. influenzae cells grown microaerobically and anaerobically in a rich medium. The data indicate that several H. influenzae metabolic proteins similar to Escherichia coli proteins, known to be regulated by low concentrations of oxygen, were well expressed in both growth conditions in H. influenzae. An in silico model of the H. influenzae metabolic network was used to study the effects of selective deletion of certain enzymatic steps. This allowed us to define proteins predicted to be essential or non-essential for cell growth and to address numerous unresolved questions about intermediary metabolism of H. influenzae. Comparison of data from in vivo protein expression with the protein list associated with a genome-scale metabolic model showed significant coverage of the known metabolic proteome. This study demonstrates the significance of an integrated approach to the characterization of H. influenzae metabolism.
authors.affiliation: Department of Bioengineering, University of California at San Diego, La Jolla, California, USA.
authors.forename: Anu
authors.initials: A
authors.lastname: Raghunathan
authors.forename: Nathan D
authors.initials: ND
authors.lastname: Price
authors.forename: Michael Y
authors.initials: MY
authors.lastname: Galperin
authors.forename: Kira S
authors.initials: KS
authors.lastname: Makarova
authors.forename: Samuel
authors.initials: S
authors.lastname: Purvine
authors.forename: Alex F
authors.initials: AF
authors.lastname: Picone
authors.forename: Tim
authors.initials: T
authors.lastname: Cherny
authors.forename: Tao
authors.initials: T
authors.lastname: Xie
authors.forename: Thomas J
authors.initials: TJ
authors.lastname: Reilly
authors.forename: Robert
authors.initials: R
authors.lastname: Munson
authors.forename: Ryan E
authors.initials: RE
authors.lastname: Tyler
authors.forename: Brian J
authors.initials: BJ
authors.lastname: Akerley
authors.forename: Arnold L
authors.initials: AL
authors.lastname: Smith
authors.forename: Bernhard O
authors.initials: BO
authors.lastname: Palsson
authors.forename: Eugene
authors.initials: E
authors.lastname: Kolker
mesh_terms: D001671:Biochemistry / Q000379:methods; D050260:Carbohydrate Metabolism; D002244:Carbon / Q000378:metabolism; D002455:Cell Division; D003470:Culture Media; D004252:DNA Mutational Analysis; D004579:Electron Transport; D004583:Electrons; D004926:Escherichia coli / Q000378:metabolism; D005285:Fermentation; D006193:Haemophilus influenzae / Q000378:metabolism*; D008954:Models, Biological; D008962:Models, Theoretical; D010100:Oxygen / Q000378:metabolism; D040081:Protein Array Analysis; D020543:Proteome; D040901:Proteomics / Q000379:methods; D014233:Tricarboxylic Acids / Q000378:metabolism
chemical_list: D003470:Culture Media; D020543:Proteome; D014233:Tricarboxylic Acids; D002244:Carbon; D010100:Oxygen