Experimental and computational assessment of conditionally essential genes in Escherichia coli.
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 approximately 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.
Joyce
Andrew R
AR
Program in Bioinformatics, University of California, San Diego, La Jolla, California 92093, USA.
Reed
Jennifer L
JL
White
Aprilfawn
A
Edwards
Robert
R
Osterman
Andrei
A
Baba
Tomoya
T
Mori
Hirotada
H
Lesely
Scott A
SA
Palsson
Bernhard Ø
BØ
Agarwalla
Sanjay
S
D001426:Bacterial Proteins / Q000032:analysis / Q000235:genetics* / Q000378:metabolism; D003198:Computer Simulation; D003470:Culture Media; D004926:Escherichia coli / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D005798:Genes, Bacterial; D005990:Glycerol; D008954:Models, Biological; D009154:Mutation; D020133:Reverse Transcriptase Polymerase Chain Reaction; D014158:Transcription, Genetic
D001426:Bacterial Proteins; D003470:Culture Media; D005990:Glycerol