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Characterizing Escherichia coli DH5α growth and metabolism in a complex medium using genome‐scale flux analysis
Author(s) -
Selvarasu Suresh,
Ow Dave SiakWei,
Lee Sang Yup,
Lee May May,
Oh Steve KahWeng,
Karimi Iftekhar A.,
Lee DongYup
Publication year - 2008
Publication title -
biotechnology and bioengineering
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.136
H-Index - 189
eISSN - 1097-0290
pISSN - 0006-3592
DOI - 10.1002/bit.22119
Subject(s) - in silico , flux balance analysis , flux (metallurgy) , escherichia coli , serine , biochemistry , biology , metabolic flux analysis , metabolism , computational biology , chemistry , gene , enzyme , organic chemistry
Genome‐scale flux analysis of Escherichia coli DH5α growth in a complex medium was performed to investigate the relationship between the uptake of various nutrients and their metabolic outcomes. During the exponential growth phase, we observed a sequential consumption order of serine, aspartate and glutamate in the complex medium as well as the complete consumption of key carbohydrate nutrients, glucose and trehalose. Based on the consumption and production rates of the measured metabolites, constraints‐based flux analysis of a genome‐scale E. coli model was then conducted to elucidate their utilization in the metabolism. The in silico analysis revealed that the cell exploited biosynthetic precursors taken up directly from the complex medium, through growth‐related anabolic pathways. This suggests that the cell could be functioning in an energetically more efficient manner by reducing the energy needed to produce amino acids. The in silico simulation also allowed us to explain the observed rapid consumption of serine: excessively consumed external serine from the complex medium was mainly converted into pyruvate and glycine, which in turn, led to the acetate accumulation. The present work demonstrates the application of an in silico modeling approach to characterizing microbial metabolism under complex medium condition. This work further illustrates the use of in silico genome‐scale analysis for developing better strategies related to improving microbial growth and enhancing the productivity of desirable metabolites. Biotechnol. Bioeng. 2009; 102: 923–934. © 2008 Wiley Periodicals, Inc.