Figure 4

The systems approach for the function of the transcription factor YiaU. (A). The genome-wide binding of YiaU across the genome. (B). Clusters of Orthologous Groups (COGs) were enriched among the differentially expressed genes between the wild type BW25113 and yiaU mutant strains. (C). The phenotypes of the E. coli BW25113 and yiaU knockout strains in the Biolog plate PM12B, measured in RPMI_10LB medium for oxacillin at 4 different doubling concentrations. yiaU mutant strain (left panel) had a negative phenotype at the highest oxacillin concentration (8X) PM12B microarray (yellow line). The other antibiotics tested at 4 different concentrations are penicillin G, tetracycline, carbenicillin, penimepicycline, polymyxin B, paromomycin, vancomycin, d,l-serine hydroxamate, sisomycin, sulfamethazine, novobiocin, 2,4-diamino-6,7-dilsopropyl-pteridine, sulfadiazine, benzethonium chloride, tobramycin, 5-fluoroorotate, spectinomycin, l-aspartic-b-hydroxamate, spiramycin, rifampicin, dodecyl trimethyl ammonium bromide. (D). The growth measurement of the wild type and yiaU mutant strains under different conditions. Left panel: M9 glucose with l-threonine. Right panel: M9 glucose with l-threonine and 0.3 M NaCl. (E) Predicted structure and YiaU regulation of waa operon, yiaT and adeP in E.coli BW25113. The differentially expressed genes are shown by a red arrow. The waa and gltBD operon promoters are shown by a black arrow.