Expression profiling of all protein‐coding genes in wild‐type and three DNA repair‐deficient substrains of Escherichia coli K‐12

Gene chips or cDNA arrays of the entire set of Escherichia coli ( E.coli ) K12 genes were used to measure the expression, at the mRNA level,of all 4290 protein‐coding genes in wild‐type (WT) and three DNA repair‐deficientderivative strains: (i) AB1157 (WT), (ii) LR39 ( ada , ogt) , (iii)MV1932 ( alkA1 , tag‐1 ) and (iv) GM5555 ( mutS) . The aimwas to investigate whether disruption of a single gene would result in significantdeviation in the expression of other genes in these organisms. We describehere a simple approach for a stringent statistical evaluation of cDNA arraydata. This includes: (i) determination of intra‐ and interassay variationcoefficients for different expression levels, (ii) rejection of biased duplicates,(iii) mathematical background determination, and (iv) comparison of expressionlevels of identical copies of a gene. The results demonstrated a highly significantcorrelation of gene expression when the mutants were individually comparedwith the wild‐type. Altogether, 81 deviations of the expression of 59 geneswere noted, out of 12,870, when 3‐fold or greater up‐ or down‐regulation wasused as a criterion of differential expression. In the light of current knowledgeof E. coli biology, the differential expression did not follow anylogical pattern. In fact, the deviations may simply represent inter‐assayvariation. The results obtained here with a simple model organism are differentfrom those obtained with most mammalian knockouts: disruption of the functionof a single gene does not, under good growth conditions, necessarily resultin great changes in the expression of other genes. Copyright ©2002 John Wiley & Sons, Ltd.