May, 2005
Data Sets
Project summary. When cultured on a mixture of glucose and lactose, E. coli grows preferentially on glucose until it is exhausted, resulting in growth arrest while the cells adjust to growth on lactose, i.e., diauxie. K-means clustering of the transcriptome dataset of wildtype E. coli during glucose-lactose diauxie revealed three regulatory networks (RpoS, Crp, and RelA) that dominated the transcription profile. Therefore, we investigated the temporal changes in transcription during glucose-lactose diauxie in the wildtype and mutants lacking the key regulators, RpoS, Crp, and RelA (ppGpp synthetase).
Culture conditions. E. coli MG1655 and isogenic mutants were cultured in a 2 l Biostat B fermentor (B. Braun Biotech International) containing 1 liter of Morpholinepropanesulfonic acid (MOPS) minimal medium with 0.5 g/l of glucose and 1.5 g/l of lactose. The temperature was maintained at 37ºC and pH was kept constant at 7.2 by the addition of 2 M NaOH. The dissolved oxygen level was maintained above 20% of saturation by adjusting the agitation speeds in the range of 400-600 rpm with fixed 1 l/min air flow. Growth was monitored as absorbance at 600nm. E. coli relA251::kanR was a gift from M. Cashel, constructed as described18. The E. coli crp::kanR and rpoS::kanR strains were constructed by allelic replacement of the entire genes.
Wildtype Diauxie 
Time (min) A600 Timepoint
780 0.143 WT_tp1
830 0.245 WT_tp2
861 0.345 WT_tp3
869 0.38 WT_tp4
878 0.406 WT_tp5
888 0.408 WT_tp6
898 0.403 WT_tp7
908 0.422 WT_tp8
919 0.446 WT_tp9
929 0.49 WT_10
939 0.534 WT_tp11
969 0.706 WT_tp12
999 0.907 WT_tp13
1035 1.344 WT_tp14
1049 1.458 WT_tp15
1070 1.594 WT_tp16
1089 1.604 WT_tp17
RpoS Mutant
Diauxie
Time (min) A600 Timepoint 120 0.257 rpoS tp1 150 0.372 rpoS tp2 160 0.391 rpoS tp3 170 0.432 rpoS tp4 180 0.434 rpoS tp5 190 0.438 rpoS tp6 200 0.472 rpoS tp7 210 0.513 rpoS tp8 220 0.561 rpoS tp9 250 0.78 rpoS tp10 290 1.21 rpoS tp11 315 1.55 rpoS tp12 330 1.63 rpoS tp13Crp Mutant Diauxie
Time (min) A600 Timepoint 0 0.054 none 60 0.078 none 120 0.098 none 180 0.134 none 210 0.168 none 240 0.216 none 250 0.24 crp tp2 300 0.319 none 315 0.353 none 330 0.378 none 345 0.415 none 360 0.455 none 375 0.503 none 390 0.532 none 405 0.56 crp tp5 420 0.568 crp tp6 450 0.56 crp tp7RelA Mutant Diauxie
Time (min) A600 Timepoint 832 0.198 tp1 865 0.283 tp2 896 0.437 tp4 909 0.53 tp5 916 0.526 tp6 925 0.526 tp7 935 0.532 tp8 945 0.535 tp9 955 0.535 tp10 966 0.582 tp11 976 0.626 tp12 1007 0.772 none 1036 0.959 none 1067 1.278 none 1095 1.479 none 1125 1.509 none 1140 1.544 none 1325 1.38 none