Experimental and Computational Assessment of Conditionally Essential Genes in Escherichia coli

Keio University, Edo, Tokyo, Japan
Journal of Bacteriology (Impact Factor: 2.81). 01/2007; 188(23):8259-71. DOI: 10.1128/JB.00740-06
Source: PubMed


Genome-wide gene essentiality data sets are becoming available for Escherichia coli, but these data sets have yet to be analyzed in the context of a genome scale model. Here, we present an integrative model-driven
analysis of the Keio E. coli mutant collection screened in this study on glycerol-supplemented minimal medium. Out of 3,888 single-deletion mutants tested,
119 mutants were unable to grow on glycerol minimal medium. These conditionally essential genes were then evaluated using
a genome scale metabolic and transcriptional-regulatory model of E. coli, and it was found that the model made the correct prediction in ∼91% of the cases. The discrepancies between model predictions
and experimental results were analyzed in detail to indicate where model improvements could be made or where the current literature
lacks an explanation for the observed phenotypes. The identified set of essential genes and their model-based analysis indicates
that our current understanding of the roles these essential genes play is relatively clear and complete. Furthermore, by analyzing
the data set in terms of metabolic subsystems across multiple genomes, we can project which metabolic pathways are likely
to play equally important roles in other organisms. Overall, this work establishes a paradigm that will drive model enhancement
while simultaneously generating hypotheses that will ultimately lead to a better understanding of the organism.

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    • "The model was modified to accommodate genetic differences between MG1655 and BW25113. Since the araBAD, rhaBAD, and lacZ genes are absent from the BW25113 strain, the associated metabolic reactions were removed (Joyce et al., 2006). The upper limits of the glucose and oxygen uptake rates were set to 10 and 0 mmol/gDCW/h, respectively, to simulate anaerobic growth on minimal glucose medium. "
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    • "Along with data obtained by high-throughput systems, modeling of metabolism by mathematical approaches has become an important tool for analyzing cell responses and unravel the metabolic regulation between the cell information/control systems [111]. Moreover, genome-scale models of metabolism have been analyzed by constraint-based approaches [123]. Gene deletion effects over flux distributions have also been studied in order to find the combination that provides the best metabolic performance on a given condition. "
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    • "The human essential genes were downloaded from the OGEE database (build: 304) (Chen et al., 2012). Because the conditional essential genes were essential only under certain circumstances (Joyce et al., 2006), these genes were not used in this study. The protein product of an essential gene was regarded as an essential protein. "
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