TABLE 1

Genes differently regulated by conditioned mediuma

GeneGene product description (old gene name)Fold change
Genes upregulated by conditioned medium
    topBDNA topoisomerase III2.6
    yddGUnknown3.0
    folCFolyl-polyglutamate synthetase2.5
Genes downregulated by conditioned medium
    abrBTranscriptional pleiotropic regulator of transition state genes2.5
    folBDihydroneopterin aldolase2.5
    yddASimilar to unknown proteins2.8
    feuCIron uptake system permease protein3.2
    feuBIron uptake system permease protein3.0
    feuAIron uptake system binding protein4.3
    yclMAspartokinase 33.0
    yclNSimilar to ferrichrome permease2.5
    yclPSimilar to ferrichrome ATP-binding protein2.1
    yclQSimilar to ferrichrome ABC transporter2.3
    ydbNPutative RNA chaperone7.5
    ydfBUncharacterized N-acetyltransferase2.5
    gabPGamma-aminobutyrate permease2.5
    yfmCFerric iron citrate-binding protein3.0
    yfiYProbable siderophore-binding lipoprotein5.3
    yfiZSimilar to iron(III) dicitrate transport permease2.3
    yhfQPutative ABC transporter substrate-binding lipoprotein3.7
    mtnKMethylthioribose kinase (ykrT)3.2
    ykuNSimilar to flavodoxin6.5
    ykuOUnknown11.3
    ykuPSimilar to flavodoxin7.5
    fruRTranscriptional repressor of the fructose operon12.1
    fruAPTS fructose-specific enzyme II ABC component13.9
    ylaDAnti-sigma YlaC factor3.7
    pyrKDihydroorotate dehydrogenase (electron transfer subunit)2.8
    AsdAspartate-semialdehyde dehydrogenase2.5
    yoaCPutative sugar kinase2.5
    yoaDPutative 2-hydroxyacid dehydrogenase3.0
    lysCAspartokinase II (alpha and beta subunits)3.5
    dhbFDimodular nonribosomal peptide synthase11.3
    dhbBIsochorismatase8.0
    dhbE2,3-Dihydroxybenzoate-AMP ligase9.8
    dhbCIsochorismate synthase12.1
    dhbA2,3-Dihydro-2,3-dihydroxybenzoate dehydrogenase8.0
    yuilSimilar to unknown proteins4.9
    homHomoserine dehydrogenase3.0
    frlBFructosamine deglycase (yurP)2.5
    fhuCFerrichrome ATP-binding protein3.2
    fhuGFerrichrome ABC transporter permease3.5
    fhuBFerrichrome ABC transporter permease3.0
    fhuDFerrichrome binding protein3.7
    ywjBSimilar to unknown proteins2.1
    ywbOSimilar to unknown proteins2.5
    efeBDeferrochelatase/peroxidase (ywbN)4.0
    efeOProbable iron uptake system component (ywbM)2.5
    efeUIron permease (ywbL)1.8
    yxeBFerric iron hydroxamate-binding protein6.1
  • a DNA microarrays were performed as described in Materials and Methods. The Statistical Analysis of Microarrays (SAM) program was used to identify genes whose expression changed 2.5-fold or more over three independent experiments with at least a 95% confidence (http://statweb.stanford.edu/~tibs/SAM/ ). Genes are arranged based on their location on the chromosome. Arrows indicate genes that are part of a known or predicted operon. The direction of each arrow indicates the genetic arrangement of the operon. Any genes that are part of a known operon but with changes in expression less than the 2.5-fold cutoff with 95% confidence are also included. Genes known to be directly regulated by the Fur repressor are in bold.