Narrow Results

Systematic studies have revealed that single gene deletions often display little phenotypic effects under laboratory conditions and that in many cases gene dispensability depends on the experimental conditions. To elucidate the environmental dependency of genes, we analyzed the effects of gene deletions by Phenotype MicroArray™ (PM), a system for quantitative screening of thousands of phenotypes in a high-throughput manner. Here, we proposed a new statistical approach to minimize error inherent in measurements of low respiration rates and find which mutants showed significant phenotypic changes in comparison to the wild-type. We show analyzing results from comprehensive PM assays of 298 single-gene knockout mutants in the Keio collection and two additional mutants under 1,920 different conditions. We focused on isozymes of these genes as simple duplications and analyzed correlations between phenotype changes and protein expression levels. Our results revealed divergence of the environmental dependency of the gene among the knockout genes and have also given some insights into possibilities of alternative pathways and availabilities of information on protein synthesis patterns to classify or predict functions of target genes from systematic phenotype screening.

Phenotype MicroArray (PM) technology is high-throughput phenotyping system [1] and is directly applicable to assay the effects of genetic changes in cells. In this study, we performed comprehensive PM analysis using single gene deletion mutants of central metabolic pathway and related genes. To elucidate the structure of central metabolic networks in Escherichia coli K-12, we focused 288 different PM conditions of carbon and nitrogen sources and performed bioinformatic analysis. For data processing, we employed noise reduction procedures. The distance between each of the mutants was defined by Manhattan distance and agglomerative Ward's hierarchical method was applied for clustering analysis. As a result, five clusters were revealed which represented to activate or repress cellular respiratory activities. Furthermore, the results might suggest that Glyceraldehyde-3P plays a key role as a molecular switch of central metabolic network.