In Silico Metabolic Model and Protein Expression of Haemophilus influenzae Strain Rd KW20 in Rich Medium.
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.
Raghunathan
Anu
A
Department of Bioengineering, University of California at San Diego, La Jolla, California, USA.
Price
Nathan D
ND
Galperin
Michael Y
MY
Makarova
Kira S
KS
Purvine
Samuel
S
Picone
Alex F
AF
Cherny
Tim
T
Xie
Tao
T
Reilly
Thomas J
TJ
Munson
Robert
R
Tyler
Ryan E
RE
Akerley
Brian J
BJ
Smith
Arnold L
AL
Palsson
Bernhard O
BO
Kolker
Eugene
E
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
D003470:Culture Media; D020543:Proteome; D014233:Tricarboxylic Acids; D002244:Carbon; D010100:Oxygen