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首页> 外文期刊>Comparative and functional genomics >Expression profiling of all protein-coding genes in wild-type and three DNA repair-deficient substrains of Escherichia coli K-12
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Expression profiling of all protein-coding genes in wild-type and three DNA repair-deficient substrains of Escherichia coli K-12

机译：所有蛋白质编码基因在大肠杆菌K-12的野生型和3个DNA修复缺陷型亚菌株中的表达谱

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摘要

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-deficient derivative strains: (i) AB1157 (WT), (ii) LR39 (ada, ogt), (iii) MV1932 (alk A1, tag-1) and (iv) GM5555 (mutS). The aim was to investigate whether disruption of a single gene would result in significant deviation in the expression of other genes in these organisms. We describe here a simple approach for a stringent statistical evaluation of cDNA array data. This includes: (i) determination of intra- and interassay variation coefficients for different expression levels, (ii) rejection of biased duplicates, (iii) mathematical background determination, and (iv) comparison of expression levels of identical copies of a gene. The results demonstrated a highly significant correlation of gene expression when the mutants were individually compared with the wild-type. Altogether, 81 deviations of the expression of 59 genes were noted, out of 12,870, when 3-fold or greater up- or down-regulation was used as a criterion of differential expression. In the light of current knowledge of E. coli biology, the differential expression did not follow any logical pattern. In fact, the deviations may simply represent inter-assay variation. The results obtained here with a simple model organism are different from those obtained with most mammalian knockouts: disruption of the function of a single gene does not, under good growth conditions, necessarily result in great changes in the expression of other genes.
机译：整套大肠杆菌（E. coli）K12基因的基因芯片或cDNA阵列用于测量野生型（WT）和3种DNA修复的所有4290种蛋白质编码基因在mRNA水平上的表达。缺陷衍生菌株：（i）AB1157（WT），（ii）LR39（ada，ogt），（iii）MV1932（alk A1，tag-1）和（iv）GM5555（mutS）。目的是研究单个基因的破坏是否会导致这些生物中其他基因表达的显着偏离。我们在这里描述了对cDNA阵列数据进行严格统计评估的一种简单方法。这包括：（i）确定不同表达水平的批内和批间变异系数，（ii）拒绝重复的重复，（iii）数学背景确定，（iv）基因相同拷贝的表达水平比较。结果表明，分别将突变体与野生型进行比较时，基因表达高度相关。当使用3倍或更高的上调或下调作为差异表达的标准时，总共注意到了12,870个中59个基因表达的81个偏差。根据目前对大肠杆菌生物学的了解，差异表达没有遵循任何逻辑模式。实际上，偏差可能只是代表批间差异。在这里，用简单的模型生物获得的结果与通过大多数哺乳动物敲除获得的结果不同：在良好的生长条件下，单个基因功能的破坏并不一定会导致其他基因表达的巨大变化。

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