Table 2

Genes most affected by the overexpression of ypdB

Geneab no.arFb (arbitrary units)Log2 ratiocPdFunctionTranscriptional regulatione
YpdBYehS
ypdBb238112,8901507.50.01Predicted response regulatorYpdB ↑ (positive control)
yhjXb35471,040304.9≤10−3Uncharacterized member of the MFS of transportersYpdB ↑
yjiYb43542,0801104.3≤10−3Predicted inner membrane proteinYpdB ↑
fhuFb43671,6705001.7≤10−3Ferric iron reductase↑↓
guaCb01042,1006701.6≤10−3GMP reductase↑↓
entCb0593250901.60.01Isochorismate synthase 1↑↓
fhuAb01501,2605701.10.01Outer membrane porin↑↓
cpxPb39131,0004901.00.01Regulator of the Cpx response↑↓
fecBb42901,2306500.9≤10−3Periplasmic substrate-binding component of the iron dicitrate ABC transporter↑↓
entEb0594110600.90.022,3-Dihydroxybenzoate-AMP ligase↑↓
ynjHb17607401,860−1.3≤10−3Hypothetical protein↑↓
ygbLb2738130340−1.4≤10−3Hypothetical protein↑↓
yahMb0327210580−1.5≤10−3Hypothetical protein↑↓
iraPb03823301,030−1.6≤10−3Antiadaptor protein for σS stabilization↑↓
ygbKb2737220690−1.70.01Hypothetical protein↑↓
yehSb21241,68016,130−3.3≤10−3Hypothetical protein↑↓ (control)
  • a Gene names/b numbers and gene product functions were taken from the EcoCyc database (http://www.ecocyc.org/) (23) and the Affymetrix Expression Analysis Sequence Information Database (27).

  • b rF, relative fluorescence (arbitrary units).

  • c Log2 ratio of transcript levels for the ypdB and yehS overexpression strains. Log2 was calculated from the ratio of the mean fluorescence intensity of the respective transcript in the ypdB overexpression strain to that measured in the yehS overexpression strain. A negative (or positive) value denotes a decrease (or increase) in transcription level upon overproduction of YpdB in comparison to that seen in the YehS-overproducing strain.

  • d P value significance (t test) of single rF values.

  • e Effect of YpdB overproduction on the transcription levels of the respective genes in E. coli MG21 cells compared to control cells (E. coli MG21/pBAD24), as determined by Northern blot analysis. YpdB-dependent induction (YpdB ↑), YpdB-independent induction/repression (↑↓), or YpdB-dependent repression (YpdB ↓) of the gene is indicated (Fig. 2A).