TABLE 2.

Promoters of genes that are upregulated in microorganisms during interaction with a eukaryotic hosta

ClassFunction and gene or fusionProtein function; possible role in host interactionsOrganismHost or environmentSelectionReference
Class I: genes involved in motility or chemotaxis
Flagellum/pilus biosynthesis
    fliIFlagellum-specific ATP synthaseV. choleraeMouseRIVET191
    fliFFlagellar M-ring proteinP. fluorescensSugar beetdapB78
    fliFFlagellar M-ring proteinS. suisPigerm254
    α-flaAAntisense transcript—subunit flagellinV. choleraeMouseRIVET32
    α-fliMAntisense transcript—flagellar C-ring protein (switch complex)P. stutzeriRicedapBa
    Rsc0726Type IV fimbrial biogenesis (PilW-related protein)R. solanacearumTomatotrpEG26
Chemotaxis
    iviIVChemotaxis receptor protein (MCP)V. choleraeMouseRIVET32
    vca0773Chemotaxis receptor protein (MCP)V. choleraeMouseRIVET191
    vc1535Chemotaxis receptor protein (MCP)V. choleraeMouseRIVET191
    trgChemotaxis receptor protein (MCP)E. chrysanthemiSpinachgfp-LA299
    cheRChemotaxis protein (methyltransferase)E. chrysanthemiSpinachgfp-LA299
    cheYTwo-component response regulatorP. aeruginosaMousepurEK290
    cheYTwo-component response regulatorR. solanacearumTomatotrpEG26
    α-cheVAntisense transcript—chemotaxis proteinV. choleraeMouseRIVET32
    α-mcpAntisense transcript—chemotaxis receptor protein (MCP)P. stutzeriRicedapB224
Class II: genes involved in nutrient scavenging
Metal ion acquisition
    Siderophore synthesis
        irp2Yersiniabactin synthetase subunit HMWP2Y. enterocoliticaMousecat300
        iucAAerobactin synthesisK. pneumoniaeMousegalU133
        entFEnterobactin synthesisS. entericaMousecat98
        rucCRuckerbactin synthesisY. ruckeriFishcat65
        pvdDPyoverdine synthetaseP. aeruginosaMouse, ratpurA93
        pvsAPyoverdine synthetaseP. fluorescensSugar beetdapB78
    Siderophore receptor and uptake
        fepAFerrienterobactin receptorK. pneumoniaeMousegalU133
        fptAPyochelin receptorP. aeruginosaMousepurEK290
        fyuAYersiniabactin receptorY. enterocoliticaMousecat300
        ufrASiderophore receptorP. fluorescensSugar beetdapB78
        foxASiderophore receptorY. enterocoliticaMousecat300
        fhuAFerric hydroxamate receptorS. entericaMousepurA98
        fhuAFerric hydroxamate receptorS. flexneriEpithelial cellsDFI233
        ivi10Putative siderophore receptorP. gingivalisMousetet298
        rupARuckerbactin receptorY. ruckeriFishcat65
        iviVIITonB complex protein (ExbB-like)Y. ruckeriFishcat65
        rupDGCSiderophore ABC transporter proteinY. ruckeriFishcat65
    Siderophore-independent iron transport
        fbpAPeriplasmic iron binding protein of ABC transporterB. abortusMacrophageDFI62
        vc0202Periplasmic iron binding protein of ABC transporterV. choleraeMouseRIVET191
        yfeAPeriplasmic (chelated) iron-binding protein of ABC transporterE. chrysanthemiSpinachgfp-LA299
        hemTPeriplasmic hemin binding protein of ABC transporterB. pseudomalleiMacrophagecatb
        hmuTPeriplasmic hemin binding protein of ABC transporterE. chrysanthemiSpinachgfp-LA299
        vc0201ATP binding protein of ABC transporterV. choleraeMouseRIVET191
        vca0687ATP binding protein of ABC transporterV. choleraeMouseRIVET191
        yfuBPermease of ABC transporterY. enterocoliticaMousecat300
        vca0203Permease of ABC transporterV. choleraeMouseRIVET191
        hmuUPermease of hemin ABC transporterE. chrysanthemiSpinachgfp-LA299
        hmuSHemin degrading proteinE. chrysanthemiSpinachgfp-LA299
        sitABCDABC transporter (Fe2+/Mn2+ uptake)S. entericaMousepurA114, 156
        sitAPeriplasmic binding protein of ABC transporter (Fe2+/Mn2+ uptake)S. flexneriEpithelial cellsDFI233, 234
        sitCPermease of ABC transporter (Fe2+/Mn2+ uptake)Y. enterocoliticaMousecat83
    Regulation of iron uptake
        np20Ferric uptake regulator (Fur)P. aeruginosaMousepurEK290
    Other
        nex10Putative K+ channelS. melilotiAlfalfa nodulesbacA188
        Rv3237cK+ channelM. tuberculosisMacrophageinhA56
        trkHK+ transport systemB. abortusMacrophageDFI62
        kupK+ uptake proteinV. choleraeMouseRIVET191
        psaBCAMn2+ uptake systemS. pneumoniaeMouseDFI160, 161
        mntHMn2+ transporterB. pseudomalleiMacrophagecatb
        mgtAMg2+ transporterS. entericaMousecat98
        mgtBMg2+ transporterS. entericaMousecat98
        ntpJNa+ translocating ATPaseS. aureusMouseRIVET152
        Rsc1951Solute/Na+ symporterR. solanacearumTomatotrpEG26
        vca2705Solute/Na+ symporterV. choleraeMouseRIVET191
        hoxQNi2+ transport/hydrogenase activityY. enterocoliticaMousecat300
Phosphate acquisition
    phoAAlkaline phosphataseS. flexneriEpithelial cellsDFI233
    phoBResponse regulator of two-component systemE. chrysanthemiSpinachgfp-LA299
    phoSPeriplasmic binding proteinS. entericaMacrophagesDFI279
    phoURegulator of transport systemE. chrysanthemiSpinachgfp-LA299
    pstSPeriplasmic binding protein of high-affinity ABC transporterS. flexneriEpithelial cellsDFI233
    pstBATP-binding protein of high-affinity ABC transporterE. chrysanthemiSpinachgfp-LA299
    phnCATP-binding protein of ABC transporterE. chrysanthemiSpinachgfp-LA299
    phnDPeriplasmic protein of ABC transporterE. chrysanthemiSpinachgfp-LA299
    vc0721Periplasmic phosphate-binding proteinV. choleraeMouseRIVET191
    ppkPolyphosphate kinaseE. chrysanthemiSpinachgfp-LA299
Sulfate acquisition
    cysAPermease of ABC transporterV. choleraeMouseRIVET32
    ssuBACABC transporterB. abortusMacrophageDFI62
    cl52TransporterL. monocytogenesMacrophageDFI295
    cysDSulfate adenylate transferaseM. tuberculosisMacrophagesDFI275
Amino acid acquisition
    Rsp1575Periplasmic binding protein of ABC transporterR. solanacearumTomatotrpEG26
    ipx46ATP-binding component of ABC transporterP. syringaeA. thalianahrcC16
    livMHPermease for high-affinity transport of branched amino acidsP. fluorescensSugar beetpanB218
    hutTPermease for histidine uptakeP. fluorescensSugar beetpanB218
    iviDAmino acid transporterS. gordoniiRabbitcat127
    sdaC2Serine transporterV. choleraeMouseRIVET191
Sugar uptake
    Phosphotransferase systems
        celBCellobiose PTS, IIL. monocytogenesMousehly77
        pts14CCellobiose PTS, IICL. plantarumMouseRIVET24
        ptsIBCASucrose PTS, EIIBCAL. plantarumMouseRIVET24
        pts32BCSucrose PTS, EIIBCL. plantarumMouseRIVET24
        vc0207Sucrose PTS, EIIBCV. choleraeMouseRIVET191
        orf5-iviLCellobiose PTSS. gordoniiRabbitcat127
        ptfAFructose PTSK. pneumoniaeMousegalU133
        ptnAMannose PTSL. monocytogenesMacrophageDFI295
        pts37ASorbitol PTS, EIIAL. plantarumMouseRIVET24
        pts19AN-Acetylglucosamine/galactosamine PTS, IIAL. plantarumMouseRIVET24
        nagEN-Acetylglucosamine PTS, IIABCE. chrysanthemiSpinachgfp-LA299
    Other sugar transporters
        malAPermease of ABC transporter for maltose uptakeS. aureusMouseRIVET152
        rbsCPermease of ABC transporter for ribose uptakeH. influenzaeChinchillaDFI164
        rbsDCytoplasmic ribose-binding proteinL. plantarumMouseRIVET24
        Rsp0536Transmembrane sugar-proton symporterR. solanacearumTomatotrpEG26
        uhpTHexose phosphate transporterS. flexneriEpithelial cellsDFI233
        rhiTRhamnogalacturonide transporterE. chrysanthemiSpinachgfp-LA299
        yicJSodium galactoside symporterE. chrysanthemiSpinachgfp-LA299
Uptake of organic acids
    dctDTwo-component response regulator of C4-dicarboxylate transportP. syringaeBeanmetXW159
    dctSTwo-component sensor of C4-dicarboxylate transportP. fluorescensSugar beetpanB218
    Rsc1598Two-component sensor (DctS-homologue)R. solanacearumTomatotrpEG26
    lldPL-lactate permeaseP. fluorescensSugar beetdapB78
    tctCTricarboxylate transportY. ruckeriFishcat65
    kgtP2α-ketoglutarate permeaseR. solanacearumTomatotrpEG26
Uptake of miscellaneous     compounds
    sapAPeptide ABC transporterH. influenzaeChinchillaDFI164
    cirAColicin I receptorS. entericaMacrophagecat98
    RT1006ATP binding component of ABC transporterS. pneumoniaeMouseDFI160
    comECompetence protein (DNA uptake)S. suisPigerm254
    potF2Putrescine transport proteinP. fluorescensSugar beetdapB78
Transport of unknown     substrates
    Structural components of ABC transporters
        ivilS. gordoniiRabbitcat127
        ivs-6S. suisPigerm254
        orf2P. putidaPhytophthora parasiticapyrB140
        orfUS. suisPigerm254
        Rsc1376R. solanacearumTomatotrpEG26
        SPIV013S. pneumoniaeMouseDFI160
        uupK. pneumoniaeMousegalU133
        pup-31E. chrysanthemiSpinachgfp-LA299
        lp_0299L. plantarumMouseRIVET24
        rhi-37P. fluorescensSugar beetdapB78
        yoaES. suisPigerm254
    Periplasmic-binding proteins
        pup-59E. chrysanthemiSpinachgfp-LA299
        p39B. abortusMacrophageDFI62
        Rsc0044R. solanacearumTomatotrpEG26
    Components of TRAP-T
        vc0488Solute-binding proteinV. choleraeMouseRIVET191
        vc1275Constituent of TRAP-T carrierV. choleraeMouseRIVET191
Class III: genes of central intracellular metabolism
Intermediary metabolism
    Glyoxylate pathway
        aceAIsocitrate lyaseM. tuberculosisMacrophageinhA56
        aceBMalate synthaseY. enterocoliticaMousecat300
        aceEPyruvate dehydrogenase subunitP. syringaeA. thalianahrcC16
        pdhCPyruvate dehydrogenase subunitM. marinumMacrophageDFI11
    TCA cycle
        sucASubunit of α-ketoglutarate dehydrogenaseV. choleraeMouseRIVET32
        fumCFumaraseR. solanacearumTomatotrpEG26
        fumCFumaraseL. monocytogenesMousehly77
        frdBFumarate reductaseY. enterocoliticaMousecat83
        ppcPhosphoenolpyruvate carboxylaseS. flexneriHeLa monolayercat14
        ppcPhosphoenolpyruvate carboxylaseV. choleraeMouseRIVET191
        ppcPhosphoenolpyruvate carboxylaseE. chrysanthemiSpinachgfp-LA299
        acnAAconitaseV. choleraeMouseRIVET191
    Glycolysis
        hre-21Pyruvate kinaseY. enterocoliticaMousecat300
    Gluconeogenesis
        pckAPhosphoenolpyruvate carboxykinaseM. tuberculosisMacrophageinhA56
        pckAPhosphoenolpyruvate carboxykinaseS. melilotiAlfalfa nodulesbacA188
    Pentose phosphate     pathway
        tal3TransaldolaseL. plantarumMouseRIVET24
        tktTransketolaseM. tuberculosisMacrophagesDFI275
        tktDeoxyxylulose 5′-phosphate synthase/transketolaseB. abortusMacrophageDFI62
        tktI-NTransketolaseL. plantarumMouseRIVET24
    Other
        enoEnolaseM. tuberculosisMacrophageinhA56
Lipid/fatty acid synthesis
    dgkDiacylglycerol kinase (diacylglycerol recycling)P. putidaP. parasiticapyrB140
    accBCBiotin carboxyl carrier proteinS. flexneriHeLa monolayercat14
    phbAAcetyl-CoA acetyltransferaseR. solanacearumTomatotrpEG26
    fadA4Acetyl-CoA acetyltransferaseM. tuberculosisMacrophageinhA56
    ephFEpoxide hydrolaseM. tuberculosisMacrophageinhA56
    cfaCyclopropane fatty acid synthase (membrane modification)S. entericaMousecat98
Lipid/fatty acid degradation
    fadBFatty acid oxidation complex (alpha-subunit)S. entericaMousecat157
    fadB1Enoyl-CoA hydrataseB. abortusMacrophageDFI62
    echA19Enoyl-CoA hydrataseM. tuberculosisMacrophageinhA56
    fadB43-Hydroxyacyl-CoA dehydrogenaseM. tuberculosisMacrophageDFI275
    Rv11443-Hydroxyacyl-CoA dehydrogenaseM. tuberculosisMacrophageinhA56
    fadDLong-chain fatty acid CoA ligaseP. syringaeA. thalianahrcC16
    fadEProbable acyl CoA dehydrogenaseP. fluorescensSugar beetdapB78
    est2AcetylesteraseL. plantarumMouseRIVET24
    lipASecreted triacylglyceride-specific lipaseV. choleraeMouseRIVET32
    lipGlycerolester hydrolaseS. aureusMouseRIVET152
Phospholipid metabolism
    aasAcyl acylglycerol phosphoethanolamine acylS. entericaMacrophagesDFI279
transferase
    licCPhosphocholine cytidyltransferaseH. influenzaeChinchillaDFI164
    glpQProtein D (lipoprotein)P. multocidaMousekan108
    eutREthanolamine operon regulatorE. chrysanthemiSpinachgfp-LA299
Sugar metabolism
    cl 143UDP-galactose epimeraseL. monocytogenesMacrophageDFI295
    rbsK3RibokinaseL. plantarumMouseRIVET24
    rbsRTranscriptional repressor of ribose operon (LacI family)K. pneumoniaeMousegalU133
    xylAXylose isomeraseP. fluorescensSugar beetpanB218
    xylAXylose isomeraseL. reuteriMouseerm285
    xylRXylose operon regulator (AraC family)L. monocytogenesMacrophageDFI295
    xylRXylose operon regulator (AraC family)E. chrysanthemiSpinachgfp-LA299
    srlDSorbitol-6-phosphate dehydrogenaseP. multocidaMousekan108
    yoxDRibitol dehydrogenaseS. aureusMouseRIVET152
    uxuAMannonate dehydrataseH. influenzaeChinchillaDFI164
    ram2α-l-RhamnosidaseL. plantarumMouseRIVET24
    pbg106-Phospho-β-glucosidaseL. plantarumMouseRIVET24
    thgA1Galactoside O-acetyltransferaseL. plantarumMouseRIVET24
    vca0242Hexulose-6-phosphate synthaseV. choleraeMouseRIVET191
    glgAGlycogen synthaseR. solanacearumTomatotrpEG26
    glgB1,4-α-Glucan branching enzymeV. choleraeMouseRIVET191
    glgXGlycogen operon proteinR. solanacearumTomatotrpEG26
    malQ4-α-GlucanotransferaseV. choleraeMouseRIVET191
    iviEExo-1,4-β-cellobiohydrolaseS. gordoniiRabbitcat127
    iviHEndo-1,3-β-glucanaseS. gordoniiRabbitcat127
Amino acid synthesis
    Arginine biosynthesis
        argAN-Acetyl glutamate synthaseV. choleraeMouseRIVET32
        argFOrnithine carbamoyl transferaseH. influenzaeChinchillaDFI164
        argGArgininosuccinate synthaseR. solanacearumTomatotrpEG26
        argGArgininosuccinate synthaseL. plantarumMouseRIVET24
        argHArgininosuccinate lyaseV. choleraeMouseRIVET191
        carABCarbamoylphosphate synthetase (arginine/pyrimidine nucleotide biosynthesis)S. entericaMousepurA156
        α-carAAntisense transcript—carbamoylphosphate synthetaseP. gingivalisMousetet298
    Aromatic amino acid biosynthesis
        aroQChorismate mutaseS. entericaMouseDFI30
        trpD3Anthranilate phosphoribosyl transferase (tryptophan biosynthesis)R. solanacearumTomatotrpEG26
        trpGAnthranilate synthase β subunit (tryptophan biosynthesis)V. choleraeMouseRIVET191
        trpRCentral regulator of tryptophan-related operonsS. flexneriHeLa monolayercat14
        pheAChorismate mutase-P/prephenate dehydratase (phenylalanine/tyrosine biosynthesis)E. chrysanthemiSpinachgfp-LA299
    Cysteine biosynthesis
        cysISulfite reductase subunitV. choleraeMouseRIVET32
        sseAThiosulfate sulfurtransferaseM. tuberculosisMacrophagesDFI275
    Histidine biosynthesis
        hisAPhosphoribosylformimino-5-aminoimidazole carboxamideV. choleraeMouseRIVET191
    ribotide isomerase
        hisBImidazole glycerol phosphate dehydrataseP. aeruginosaMousepurEK290
        hisBImidazole glycerol phosphate dehydrataseH. influenzaeChinchillaDFI164
    Branched amino acid biosynthesis
        ilvAThreonine deaminase (isoleucine biosynthesis)A. pleuropneumoniaePigribBAH76
        ilvAThreonine deaminase (isoleucine biosynthesis)P. aeruginosaMousepurEK290
        ilvIAcetolactate synthase subunitA. pleuropneumoniaePigribBAH76
        ilvIAcetolactate synthase subunitP. fluorescensSugar beetdapB78
        ilvlAcetolactate synthase subunitP. syringaeA. thalianahrcC16
    Lysine biosynthesis
        lysADiaminopimelate decarboxylaseK. pneumoniaeMousegalU133
        lysADiaminopimelate decarboxylaseS. flexneriEpithelial cellsDFI233
        dcdADiaminopimelate decarboxylase (LysA homologue)P. syringaeA. thalianahrcC16
        dapCN-Succinyldiaminopimelate aminotransferaseR. solanacearumTomatotrpEG26
    Methionine biosynthesis
        metLAspartokinase/homoserine reductase (homoserine biosynthesis)Y. enterocoliticaMousecat83
        50-55S3Homoserine-O-acetyltransferaseH. capsulatumMacrophageURA5226
        cysCHomoserine-O-acetyltransferaseH. capsulatumMouseURA5226
        metRTranscription regulator (LysR family)E. chrysanthemiSpinachgfp-LA299
    Proline biosynthesis
        proCPyrroline-5-carboxylate reductaseM. tuberculosisMacrophageinhA56
        proAGlutamate-5-semialdehyde dehydrogenaseL. plantarumMouseRIVET24
    Threonine biosynthesis
        thrCThreonine synthaseS. suisPigerm254
        tdcATranscriptional activator of tdc operonK. pneumoniaeMousegalU133
    Glutamate/aspartate biosynthesis
        gltB1Glutamate synthase (large subunit)V. choleraeMouseRIVET191
        gdhAGlutamate dehydrogenaseR. solanacearumTomatotrpEG26
        ansACytoplasmic l-asparaginase IE. chrysanthemiSpinachgfp-LA299
Amino acid degradation
    gcvPGlycine cleavage system (P protein)R. solanacearumTomatotrpEG26
    gcvH1Glycine cleavage system (H protein)P. syringaeA. thalianahrcC16
    gcsH1Glycine cleavage system (H protein)L. plantarumMouseRIVET24
Nucleotide synthesis
    De novo synthesis of pyrimidine nucleotides
        pyrGCTP synthaseR. solanacearumTomatotrpEG26
        dutDeoxyuridine triphosphataseM. tuberculosisMacrophageinhA56
        rsuA16S rRNA pseudouridylate synthaseL. plantarumMouseRIVET24
    De novo synthesis of     purine nucleotides
        purFAmidophosphoribosyltransferaseR. solanacearumTomatotrpEG26
        purCPhosphoribosylaminoimidazole-Succinocarboxamide synthaseS. pneumoniaeMouseDFI160
        purEPhosphoribosylaminoimidazole carboxylase subunitH. influenzaeChinchillaDFI164
        adkAdenylate kinaseL. plantarumMouseRIVET24
        α-ivi12Antisense transcript— phosphoribosylglycinamide formyltransferaseP. gingivalisMousetet298
    Salvage pathways
        uppUracil phosphoribosyltransferaseE. chrysanthemiSpinachgfp-LA299
        Rsc0204Thymidine/pyrimidine-nucleoside phosphorylaseR. solanacearumTomatotrpEG26
        udp-1Uridine phosphorylaseV. choleraeMouseRIVET191
        udk-dcdUridine kinase/dCTP deaminaseP. multocidaMousekan108
        xdhAXanthine dehydrogenaseR. solanacearumTomatotrpEG26
        lp_0696Cytosine/adenosine deaminaseL. plantarumMouseRIVET24
Peptide and protein     synthesis
    Nonribosomal peptide synthesis
        P163Peptide synthetaseM. marinumMacrophageDFI11
        Rsp1419Peptide synthetaseR. solanacearumTomatotrpEG26
    Ribosomal synthesis
        fusA2Elongation factor GM. tuberculosisMacrophageinhA56
        EF-TuElongation factor TuL. monocytogenesMacrophageDFI295
        rrfRibosome recycling factorS. aureusMouseRIVET152
        prfB-NPeptide chain release factor 2 (N-terminal fragment)L. plantarumMouseRIVET24
        prfB-CPeptide chain release factor 2 (C-terminal fragment)L. plantarumMouseRIVET24
        α-prfCAntisense transcript—peptide chain release factor 3R. solanacearumTomatotrpEG26
        dbpADEAD-type RNA helicaseP. aeruginosaMousepurEK290
        tgtQueuine-tRNA ribosyltransferaseY. enterocoliticaMousecat300
        α-cii61Antisense transcript—16S rRNA geneP. stutzeriRicedapBa
    Amino acid tRNA         synthetases
        alaSAlanyl-tRNA synthetaseR. solanacearumTomatotrpEG26
        argSArginyl-tRNA synthetaseM. marinumMacrophageDFI11
        cysSCysteinyl-tRNA synthetaseE. chrysanthemiSpinachgfp-LA299
        glnSGlutaminyl-tRNA synthetaseR. solanacearumTomatotrpEG26
        pheSTPhenylalanyl-tRNA synthetaseS. entericaMousepurA156
        tyrSTyrosyl-tRNA synthetaseR. solanacearumTomatotrpEG26
        gatAGlu-tRNA (gln) amidotransferase (subunit A)R. solanacearumTomatotrpEG26
    Protein folding
        ppiAPeptidyl prolyl cis-trans isomerase AK. pneumoniaeMousegalU133
        groEL5ChaperonineS. melilotiAlfalfa nodulesbacA188
        dsbBDisulfide oxidoreductaseH. influenzaeChinchillaDFI164
        dsbDThiol-disulfide interchange proteinP. multocidaMousekan108
Protein degradation
    pepNAminopeptidase NR. solanacearumTomatotrpEG26
    Rsp0196Prolyl aminopeptidaseR. solanacearumTomatotrpEG26
    ipx41CarboxypeptidaseP. syringaeA. thalianahrcC16
    Rsc1476CarboxypeptidaseR. solanacearumTomatotrpEG26
    pepD1DipeptidaseL. plantarumMouseRIVET24
    P238Zinc metalloproteaseM. marinumMacrophageDFI11
    ipc017Zinc metalloproteaseS. pneumoniaeMouseDFI160
    hrePProteaseY. enterocoliticaMousecat300
    IPC001Serine proteaseS. pneumoniaeMouseDFI160
    Rsp0603Serine proteaseR. solanacearumTomatotrpEG26
    Rsc3101Serine proteaseR. solanacearumTomatotrpEG26
    α-Rsc2654Antisense transcript—serine proteaseR. solanacearumTomatotrpEG26
    Rsc3101Serine proteaseR. solanacearumTomatotrpEG26
    lonATP-dependent proteaseR. solanacearumTomatotrpEG26
    clpCATP-dependent protease Clp (ATPase subunit)L. plantarumMouseRIVET24
Cofactor biosynthesis
    Biotin biosynthesis
        bioAS-Adenosylmethionine-8-amino-7-oxononanoate aminotransferaseS. flexneriEpithelial cellsDFI233
        bioAS-Adenosylmethionine-8-amino-7-oxononanoate aminotransferaseV. choleraeMouseRIVET191
        Rsc0082S-Adenosylmethionine-8-amino-7-oxononanoate aminotransferaseR. solanacearumTomatotrpEG26
        bioHBiotin synthaseY. enterocoliticaMousecat83
        birA2Repressor of biotin ligase and biotin operonL. plantarumMouseRIVET24
    Fe-S cluster biosynthesis
        sufAFe-S cluster maturation proteinS. flexneriEpithelial cellsDFI233
        nifSCysteine desulfurase (synthesis nitrogenase metallocluster)S. melilotiAlfalfa nodulesbacA188
    Nucleotide cofactor biosynthesis
        nadENH3-dependent NAD+ synthetaseP. gingivalisMousetet298
        Rsc2193Nicotinate nucleotide adenylyltransferaseR. solanacearumTomatotrpEG26
        ribB3,4-Dihydroxy-2-butanone 4-phosphate synthaseH. influenzaeChinchillaDFI164
        ribC2Bifunctional riboflavin kinase and FMN adenylyltransferaeL. plantarumMouseRIVET24
        pncAPyrazinamidase/nicotinamidaseE. chrysanthemiSpinachgfp-LA299
    Tetrapyrrole synthesis
        hemAHeme synthesisS. entericaMousepurA98
        hemBδ-Aminolevulinic acid dehydrataseR. solanacearumTomatotrpEG26
        hemDHeme synthesisY. enterocoliticaMousecat300
        cii-11Putative tetrapyrrole methylase (PA4422 homologue)P. stutzeriRicedapB224
    Thiamine biosynthesis
        thiEThiamine phosphate pyrophosphataseR. leguminosarumPea nutDFI3
        thiFAdenylation of ThiSV. choleraeMouseRIVET191
        ipx45LipoproteinP. syringaeA. thalianahrcC16
    Biosynthesis of other         cofactors
        moeZPutative molybdopterin biosynthetic enzymeM. tuberculosisMacrophagesDFI275
        nadB2l-Aspartate oxidase (quinolinate biosynthesis)R. solanacearumTomatotrpEG26
        HI1647Pyridoxine biosynthesis proteinH. influenzaeChinchillaDFI164
        folBDihydroneopterin aldolase (folate biosynthesis)E. chrysanthemiSpinachgfp-LA299
        SPIV021FlavodoxinS. pneumoniaeMouseDFI160
Conversion of     miscellaneous or     unknown compounds
    dhaT1,3-Propanediol dehydrogenaseL. plantarumMouseRIVET24
    mdcAMalonate decarboxylaseP. fluorescensSugar beetdapB78
    glcFGlycolate oxidase (Fe-S subunit)R. solanacearumTomatotrpEG26
    gphPhosphoglycolate phosphataseR. solanacearumTomatotrpEG26
    rhi-4MorB-like reductase (complex N-compounds)P. fluorescensSugar beetpanB218
    adhEBifunctional alcohol and acetaldehyde dehydrogenaseL. plantarumMouseRIVET24
    vanRTranscriptional regulator of GntR family (aromatic compounds)P. fluorescensSugar beetdapB78
    pcaCCarboxymuconolactone decarboxylase (aromatic compounds)P. stutzeriRicedapB224
    gabD1Succinate semialdehyde dehydrogenase (putrescine degradation)R. solanacearumTomatotrpEG26
    SPIV0224-Oxalocrotonate tautomeraseS. pneumoniaeMouseDFI160
    ipx 39Haloacid dehalogenase-like hydrolaseP. syringaeA. thalianahrcC16
    pup-28DioxygenaseE. chrysanthemiSpinachgfp-LA299
    yiaKPutative dehydrogenaseP. multocidaMousekan108
    rhi-74Putative amidohydrolase (plant nitrilase-like)P. fluorescensSugar beetdapB78
    39B6MocC-like oxidoreductase (opine-like compounds)B. abortusMacrophageDFI62
Energy metabolism
    Rsc0087NADH dehydrogenaseR. solanacearumTomatotrpEG26
    nex8NADH-ubiquinone oxidoreductase subunitS. melilotiAlfalfa nodulesbacA188
    ivs-18NADH oxidaseS. suisPigerm254
    Rsc1280Transmembrane 4Fe-S ferredoxinR. solanacearumTomatotrpEG26
    α-Rsc0329Antisense transcript—ferredoxin 2Fe-SR. solanacearumTomatotrpEG26
    atpDATP synthase subunitS. aureusMouseRIVET152
    phaZPHB depolymeraseR. solanacearumTomatotrpEG26
Class IV: genes involved in stress response and adaptation
Oxidative stress
    Glutathione and     thioredoxin     metabolism
        gshGlutathione synthetaseY. enterocoliticaMousecat300
        Rsc2501γ-GlutamyltranspeptidaseR. solanacearumTomatotrpEG26
        lsfAGlutathione peroxidaseP. fluorescensSugar beetpanB218
        orf6-iviMGlutathione reductaseS. gordoniiRabbitcat127
        ydhDGlutaredoxinY. enterocoliticaMousecat300
        trxCThioredoxin IIV. choleraeMouseRIVET191
        ykmAGlutathione peroxidaseP. fluorescensSugar beetpanB218
    Peroxidases/catalases
        bcpBacterioferritin co-migratory protein (peroxidase)R. solanacearumTomatotrpEG26
        bcpPeroxidaseP. stutzeriRicedapB224
        Rsc2800PeroxidaseR. solanacearumTomatotrpEG26
        nex1PeroxiredoxinS. melilotiAlfalfa nodulesbacA188
        ohrOrganic hydroperoxide reductaseA. pleuropneumoniaePigribBAH76
        catFCatalaseP. syringaeA. thalianahrcC16
    Other
        Rsp1530l-Ascorbate oxidaseR. solanacearumTomatotrpEG26
        msrAPeptide methionine sulfoxide reductaseE. chrysanthemiSpinachgfp-LA299
        msrBPeptide methionine sulfoxide reductaseL. reuteriMouseerm285
        orf4-iviKPeptide methionine sulfoxide reductaseS. gordoniiRabbitcat127
        vc1500PqiA family proteinV. choleraeMouseRIVET191
        pqiBParaquat-inducible proteinP. fluorescensSugar beetdapB78
        oxyRRegulator (LysR family)S. suisPigerm254
        soxRTwo-component response regulatorP. aeruginosaBurned mousepurEK92
        indAIndigoidine biosynthesis protein IndAE. chrysanthemiSpinachgfp-LA299
Acid tolerance
    cadALysine decarboxylase; cadaverine synthesisV. choleraeRabbit, mouseRIVET32,174
    cadCTranscriptional regulator of cadaverine synthesis (OmpR family)S. entericaMousepurA98
    speFOrnithine decarboxylase (polyamine synthesis)P. multocidaMousekan108
    spe2S-Adenosylmethionine decarboxylase (polyamine synthesis)H. capsulatumMouseURA5226
    ureHUrease accessory proteinH. influenzaeChinchillaDFI164
Osmoregulation
    mdoGSynthesis of periplasmic β-glucansR. solanacearumTomatotrpEG26
    mdoHSynthesis of periplasmic β-glucansY. enterocoliticaMousecat300
    ndvBCyclic β-(1,2) glucan synthaseR. leguminosarumPeanutDFI3
    otsATrehalose synthetaseS. entericaMousepurA98
Low oxygen
    nrfEFormate-dependent nitrite reduction proteinP. multocidaMousekan19,108
    hemBPorphobilinogen synthaseS. flexneriHeLa monolayercat14
    nirTRespiratory nitrite reductaseV. choleraeMouseRIVET32
    Rsc2859Putative formate dehydrogenaseR. solanacearumTomatotrpEG26
Detoxification
    Metal ion efflux and homeostasis
        cutCCopper homeostasis proteinE. chrysanthemiSpinachgfp-LA299
        copACopper transporting ATPaseL. plantarumMouseRIVET24
        copACopper transporting ATPaseS. aureusMouseRIVET152
        copRSTwo-component response regulator of copper resistanceP. fluorescensSugar beetpanB218
        ragCCation efflux proteinP. fluorescensSugar beetpanB218
        lp_3288Cation efflux proteinL. plantarumMouseRIVET24
        Rsp1597Putative cation efflux pumpR. solanacearumTomatotrpEG26
        czcSTwo-component sensor kinase for regulation of Zn, Co, Cd resistanceR. solanacearumTomatotrpEG26
        iviXHeavy metal transportS. entericaMousecat98
        ipx33Metal transporting P-type ATPaseP. syringaeA. thalianahrcC16
    Antibiotic resistance
        Rsc1323Multidrug resistance proteinR. solanacearumTomatotrpEG26
        P155Drug efflux pumpM. marinumMacrophageDFI11
        lp_3303Multidrug transport proteinL. plantarumMouseRIVET24
        acrAPeriplasmic component of RND-type efflux pumpR. solanacearumTomatotrpEG26
        acrFTransmembrane protein of RND-type efflux pumpP. fluorescensSugar beetdapB78
        acrRTranscriptional regulator (TetR)Y. enterocoliticaMousecat300
        rosATransmembrane protein (fosmidomycin resistance)P. fluorescensSugar beetpanB218
        α-Rsc3205Antisense transcript—transmembrane proteinR. solanacearumTomatotrpEG26
        aphAminoglycoside 3′ phosphotransferaseM. tuberculosisMacrophageinhA56
        ydhCDrug resistance proteinY. ruckeriFishcat65
        pmrBRegulator (polymyxin resistance)S. entericaMousecat90,98
    Methylglyoxal detoxification
        ycbLGlyoxylase II enzym familyP. fluorescensSugar beetpanB218
        glxILactoylglutathione lyaseB. abortusMacrophageDFI62
    Bacteriocin autoimmunity
        plnIBacteriocin (plantaricin) immunity proteinL. plantarumMouseRIVET24
Other stress-related     proteins
    cspDCold shock-like proteinH. influenzaeChinchillaDFI164
    hslUStress-inducible protease (ATPase component)S. entericaMacrophagesDFI279
    hslUStress-inducible protease (ATPase component)R. solanacearumTomatotrpEG26
    grpEHeat shock protein 24R. solanacearumTomatotrpEG26
    yhbHRpoN modulator protein; nutritional adaptationP. stutzeriRicedapB224
    ynaFUniversal stress proteinE. chrysanthemiSpinachgfp-LA299
    ndkNucleoside diphosphate kinase (alarmone synthesis)S. entericaMousepurA98
    dinFDNA damage-inducible transmembrane protein (SOS response)R. solanacearumTomatotrpEG26
Class V: genes involved in regulation
Two-component regulatory     systems
    vsrBRegulatorR. solanacearumTomatotrpEG26
    vieBRegulatorV. choleraeMouseRIVET32
    phoPRegulatorS. entericaMousepurA98
    ivs-25RegulatorS. suisPigerm254
    pehRRegulatorR. solanacearumTomatotrpEG26
    sapRRegulatorS. suisPigerm254
    gacARegulatorY. enterocoliticaMousecat83
    Rsc1597Regulator (LuxR-like)R. solanacearumTomatotrpEG26
    vsrDRegulator (LuxR-like)R. solanacearumTomatotrpEG26
    ipx48SensorP. syringaeA. thalianahrcC16
    ipx49SensorP. syringaeA. thalianahrcC16
    vc0622SensorV. choleraeMouseRIVET191
    α-phoRAntisense transcript—sensor (virulence)L. monocytogenesMousehly55
Transcriptional regulators
    argRRepressor (AraC family)H. influenzaeChinchillaDFI164
    iviGRegulator (AraC family)S. gordoniiRabbitcat127
    lp_3646Regulator (AraC family)L. plantarumMouseRIVET24
    glpRRepressor (DeoR family)H. influenzaeChinchillaDFI164
    cpsYRegulator (LysR family)S. suisPigerm254
    Rsc2094Regulator (LysR family)R. solanacearumTomatotrpEG26
    Rsp1574Regulator (LysR family)R. solanacearumTomatotrpEG26
    yeiERegulator (LysR family)Y. enterocoliticaMousecat300
    tfdTRegulator (LysR family)P. aeruginosaMousepurEK290
    Rsp1644Regulator (MarR family)R. solanacearumTomatotrpEG26
    srpSRegulator (Crp family)E. chrysanthemiSpinachgfp-LA299
    pup-24Regulator (Cro/CI family)E. chrysanthemiSpinachgfp-LA299
    crpCRP regulatorE. chrysanthemiSpinachgfp-LA299
    relBRelB proteinE. chrysanthemiSpinachgfp-LA299
    nex7Regulator (TspO/MBR family)S. melilotiAlfalfa nodulesbacA188
    rhi-1Putative repressor (DnrO-like)P. fluorescensSugar beetpanB218
    Rv0549cPutative regulatorM. tuberculosisMacrophageinhA56
    orf1-iviBRegulator (Rgg-like)S. gordoniiRabbitcat127
    Rsc0280Regulator (MerR family)R. solanacearumTomatotrpEG26
    Rsc1997Regulator (GntR family)R. solanacearumTomatotrpEG26
Serine/threonine protein     kinases
    iviJS. gordoniiRabbitcat127
    ppkAP. aeruginosaMousepurEK288, 290
    pkn2L. plantarumMouseRIVET24
    α-lu1Antisense transcriptH. capsulatumMouseURA5226
Transcription factors
    greATranscription elongation factorR. solanacearumTomatotrpEG26
    hrpAATP-dependent RNA helicaseR. solanacearumTomatotrpEG26
    infCInitiation factor 3M. tuberculosisMacrophageinhA56
    rpoSSigma factor σ54R. solanacearumTomatotrpEG26
    Rsp1668σ54-interacting proteinR. solanacearumTomatotrpEG26
    himAIHF subunitS. entericaMacrophagesDFI279
    himAIHF subunitS. entericaMacrophagespurA156
    ihfBIHF subunitH. influenzaeChinchillaDFI164
    nusGAntitermination and rho-dependent terminationA. pleuropneumoniaePigribBAH76
    bglG4AntiterminationL. plantarumMouseRIVET24
    map 25WhiB-like putative transcription factorM. marinumMacrophageDFI221
Other
    hfqGlobal regulatorP. stutzeriRicedapB224
    hflXLocated in mutL-hfq superoperonY. enterocoliticaMousecat300
    ack-ptaAcetate kinase/phosphotransacetylaseP. multocidaMousekan108
    ptaPhosphotransacetylaseP. stutzeriRicedapB224
    agrAAccessory gene regulator; virulence regulatorS. aureusMouseRIVET152
    aldRInhibitor of protein synthesis (cleavage of mRNA)S. suisPigerm254
    cpdP3′-5′ cAMP phosphodiesteraseY. enterocoliticaMousecat300
    vc0130c-di-GMP metabolismV. choleraeMouseRIVET191
    pup-44Zn-finger-containing proteinE. chrysanthemiSpinachgfp-LA299
Class VI: genes involved in cell envelope structure and modification
Peptidoglycan
    sltYLytic transglycosylaseS. flexneriHeLa monolayercat14
    ipx10Lytic transglycosylaseP. syringaeA. thalianahrcC16
    mtgATransglycosylaseB. abortusMacrophageDFI62
    vc2487TransglycosylaseV. choleraeMouseRIVET191
    pup-36Membrane protein with C-terminal transglycosylase domainE. chrysanthemiSpinachgfp-LA299
    yvyHN-Acetyl glucosamine epimeraseL. monocytogenesMousehly55
    murCUDP-N-acetylmuramoyl-L-alanine synthetaseS. aureusMouseRIVET152
    atlN-Acetyl-muramoyl-L-alanine amidaseS. aureusMouseRIVET152
    Rv3717N-Acetyl-muramoyl-L-alanine amidaseM. tuberculosisMacrophageinhA56
    ampGMuropeptide transporterP. syringaeA. thalianahrcC16
    pup-33Periplasmic murein peptide-binding protein of ABC transporterE. chrysanthemiSpinachgfp-LA299
    pbp2Penicilline-binding protein 2S. aureusMouseRIVET152
    yrbHPutative sugar isomeraseS. flexneriHeLa monolayercat14
LPS/EPS biosynthesis
    orf3-iviFADP-l-glycero-d-mannoheptose-6-epimeraseS. gordoniiRabbitcat127
    rffGdTDP-glucose 4,6-dehydrataseY. enterocoliticaMousecat83
    manBPhosphomannomutaseY. enterocoliticaMousecat83
    mrpPutative ATPaseA. pleuropneumoniaePigribBAH76
    rfbLipopolysaccharide synthesisS. entericaMousepurA156
    algAAlginate biosynthesisP. syringaeA. thalianahrcC16
Adhesion/invasion
    hag2HemagglutininP. aeruginosaMouse, ratpurA93
    hagBHemagglutininP. gingivalisMousetet141
    hagCHemagglutininP. gingivalisMousetet141
    iviIVPutative hemagglutininY. ruckeriFishcat65
    iviVI-ATia-like proteinS. entericaMousecat98
    iviVI-BPfEMP1-like proteinS. entericaMousecat98
    flpAFibronectin/fibrinogen-binding proteinS. suisPigerm254
    nex18Putative fasciclin-like adhesion moleculeS. melilotiAlfalfa nodulesbacA188
    iviXIIITadD-like proteinY. ruckeriFishcat65
    tcpAPilin subunit of toxin-coregulated pilusV. choleraeMouseRIVET139
Outer membrane protein     (gram-negative     bacteria)
        lolAOuter membrane lipoprotein carrier proteinH. influenzaeChinchillaDFI164
        pcpLipoproteinP. multocidaMousekan108
        lppMLipoproteinM. tuberculosisMacrophageinhA56
        lppBLipoproteinH. influenzaeChinchillaDFI164
        Rsc1627LipoproteinR. solanacearumTomatotrpEG26
        sif15Outer membrane proteinY. enterocoliticaMousecat83,300
        ompWOuter membrane proteinR. solanacearumTomatotrpEG26
        pup-38Outer membrane proteinE. chrysanthemiSpinachgfp-LA299
        wssECellulose synthase subunitP. fluorescensSugar beetdapB78
        vca1008PorinV. choleraeMouseRIVET32,192
        oprD2PorinP. putidaP. parasiticapyrB140
        α-oprEAntisense transcript—porinP. aeruginosaMousepurEK290
Cell surface proteins     (gram-positive     bacteria)
        lp_0800L. plantarumMouseRIVET24
        lp_2940L. plantarumMouseRIVET24
        lp_1403L. plantarumMouseRIVET24
        lp_0141L. plantarumMouseRIVET24
Class VII: genes involved in virulence and secretion
Secretion
    SRP pathway
        tigTrigger factorP. fluorescensSugar beetpanB218
    General secretory pathway
        ftsYDocking proteinP. aeruginosaMouse, ratpurA93
        secATranslocation ATPaseS. melilotiAlfalfa nodulesbacA188
        secECytoplasmic membrane proteinA. pleuropneumoniaePigribBAH76
        outFGComponent of Out systemE. chrysanthemiSpinachgfp-LA299
        gspKType II secretory proteinR. solanacearumTomatotrpEG26
        spsABSignal peptidaseS. aureusMouseRIVET152
        orf104Signal peptidaseL. monocytogenesMousehly55
        α-cg316Antisense transcript—signal peptidaseL. monocytogenesMousehly55
    TTSS structural     components
        ssaHS. entericaMacrophagesDFI279
        hrcCR. solanacearumTomatotrpEG26
        hrpKP. syringaeA. thalianahrcC16
        hrpJP. syringaeA. thalianahrcC16
        hrpGP. syringaeA. thalianahrcC16
        hrcQbP. syringaeA. thalianahrcC16
        hrpAP. syringaeA. thalianahrcC16
        hrpAE. chrysanthemiSpinachgfp-LA299
        hrpBE. chrysanthemiSpinachgfp-LA299
        hrcCP. fluorescensSugar beetpanB218
    TTSS effector proteins
        pipBGlycolipid biosynthesisS. entericaMouseDFI30
        sifAEssential virulence factorS. entericaMouseDFI30
        avrPphDP. syringaeA. thalianahrcC16
        avrPpiBP. syringaeA. thalianahrcC16
        virPphAP. syringaeA. thalianahrcC16
        dspAE. chrysanthemiSpinachgfp-LA299
        dspEE. chrysanthemiSpinachgfp-LA299
    TTSS regulatory proteins
        ptrAInhibitor of transcriptional activator ExsAP. aeruginosaBurned mousepurEK91, 92
Virulence factors
    yhdPHemolysin-like protein (erythrocyte lysis)L. monocytogenesMacrophageDFI295
    shlBHemolysin activator proteinY. ruckeriFishcat65
    plcAPhosphatidylinositol phospholipase CL. monocytogenesMousehly55
    ispAHemolysin A homologueL. plantarumMouseRIVET24
    ctxACatalytical subunit of CT (toxine) synthesisV. choleraeMouseRIVET139
    spvBVirulence factorS. entericaMousecat98
    mig-5Virulence plasmid lipoproteinS. entericaMacrophagesDFI279
    α-mviMAntisense transcript—virulence factorL. monocytogenesMousehly55
    actAActin recruitement and polymerisation proteinL. monocytogenesMacrophageDFI295
    excPlasmid extrusion protein (TraT-like)S. entericaMacrophagesDFI279
    ivi11Immunoreactive antigenP. gingivalisMousetet298
    lpxAAcyltransferaseY. enterocoliticaMousecat300
    plyDPectin lyaseP. syringaeA. thalianahrcC16
    pmeMembrane-bound pectinesteraseR. solanacearumTomatotrpEG26
    oglOligogalacturonate lyaseE. chrysanthemiSpinachgfp-LA299
    syrESyringomycin synthetase (phytotoxin production)P. syringaeA. thalianahrcC16
    cfl-cfaCoronatine biosynthesis (phytotoxin production)P. syringaeA. thalianahrcC16
    pup-29MsgA-like virulence proteinE. chrysanthemiSpinachgfp-LA299
    ivs-21Extracellular proteinS. suisPigerm254
    SAP2Secreted proteaseC. albicansMouseRIVET262
    Rv2224cSecreted proteaseM. tuberculosisMacrophageinhA56
    map 24PE-PGRS virulence proteinM. marinumMacrophageDFI221
    map 85PE-PGRS proteinM. marinumMacrophageDFI221
    vc2621Extracellular nuclease-related proteinV. choleraeMouseRIVET191
    iaaMTryptophan 2-monooxygenase (auxin biosynthesis)E. chrysanthemiSpinachgfp-LA299
    vc1619.1Putative RTX toxinV. choleraeMouseRIVET191
Regulation
    bvrAAntiterminator of bvrBC, which encodes β-glucoside-specific permeaseL. monocytogenesMacrophageDFI295
    vacBRNA processingS. entericaMousepurA98
    vacCRNA processingS. entericaMousepurA98
    vacCRNA processingY. enterocoliticaMousecat300
    chvDTwo-component response regulatorS. entericaMousepurA98
    virBRegulator virulence genes (ParB-type)S. flexneriHeLa monolayercat14
Class VIII: genes involved in nucleic acid metabolism
DNA synthesis
    iviCSubunit of DNA polymerase IIIS. gordoniiRabbitcat127
    dnaNSubunit of DNA polymerase IIIR. solanacearumTomatotrpEG26
    dnaXSubunit of DNA polymerase IIIL. plantarumMouseRIVET24
    traIRelaxaseY. ruckeriFishcat65
DNA topology
    gyrASubunit of DNA gyraseK. pneumoniaeMousegalU133
    topBDNA topoisomerase IIIL. monocytogenesMousehly77
    RTI004DNA topoisomerase IVS. pneumoniaeMouseDFI160
    rhlBHelicaseY. enterocoliticaMousecat83
    helAHelicaseP. fluorescensSugar beetdapB302
    helBHelicaseP. fluorescensSugar beetdapB302
    helCHelicaseP. fluorescensSugar beetdapB302
DNA repair
    alkAMethyladenine DNA glycosylaseS. flexneriHeLa monolayerasd244
    udgUracil DNA glycosylaseL. monocytogenesMacrophageDFI295
    mutLDNA mismatch repair proteinY. enterocoliticaMousecat300
    uvrASubunit exonuclease ABCR. solanacearumTomatotrpEG26
    uvrBSubunit exonuclease ABCP. gingivalisMousetet298
    uvrCSubunit exonuclease ABCM. tuberculosisMacrophageinhA56
    recBSubunit of exodeoxyribonucleaseY. enterocoliticaMousecat300
    recDSubunit of exodeoxyribonucleaseS. entericaMousecat98
    recGDNA helicaseH. influenzaeChinchillaDFI164
DNA methylation
    metMethyltransferaseL. monocytogenesMousehly77
    cl 136MethyltransferaseL. monocytogenesMacrophageDFI295
    mtpSDNA methylaseY. enterocoliticaMousecat300
RNA degradation
    ornOligoribonucleaseP. fluorescensSugar beetdapB303
    rbnRNase BNV. choleraeMouseRIVET191
Cell division
    SPSpoJChromosome segregation proteinS. pneumoniaeMouseDFI160
    ispZSeptation proteinH. influenzaeChinchillaDFI164
    mukFChromosome partition proteinH. influenzaeChinchillaDFI164
    crcBChromosome condensation proteinE. chrysanthemiSpinachgfp-LA299
Class IX: genes involved in transposition and site-specific recombination
Mobile DNA elements
    IS600Transposase (family 8)S. flexneriEpithelial cellsDFI233
    tnpATransposase (family 11; IS4-like)P. syringaeA. thalianahrcC16
    ivs-8Transposase (family 11)S. suisPigerm254
    tnpATransposase (family 17; IS200-like)E. chrysanthemiSpinachgfp-LA299
    tnpTransposase (Tn5-like)Y. enterocoliticaMousecat300
    ivs-1Putative transposaseS. suisPigerm254
    iviAPutative transposaseS. gordoniiRabbitcat127
    issfl4Insertion sequenceS. flexneriHeLa monolayercat14
    tnpFIS2-likeS. flexneriHeLa monolayercat14
    ivi5IS195-likeP. gingivalisMousetet298
    gipAIS891-likeS. entericaMousepurA264
    vgrGVgr-like protein (located on multicopy genetic elements)E. chrysanthemiSpinachgfp-LA299
    vgrGVgr-like protein (located on multicopy genetic elements)B. pseudomalleiMacrophagecatb
Integrases/recombinases
    Rsp1303IntegraseR. solanacearumTomatotrpEG26
    rinAIntegrase gene activatorS. aureusMouseRIVET152
    redFResolvaseP. aeruginosaMousepurEK290
    xerDSite-specific DNA recombinaseP. syringaeBeanmetXW159
    xerDSite-specific DNA recombinaseB. abortusMacrophageDFI62
    xerDSite-specific DNA recombinaseV. choleraeMouseRIVET191
    codVIntegrase/recombinaseL. plantarumMouseRIVET24
  • a Overview of promoters of genes or operons that are upregulated in microorganisms during their interaction with a eukaryotic host, isolated with the promoter-trapping techniques IVET and DFI. The (predicted) cellular function of the corresponding microbial gene product(s) in the respective environmental niche is indicated. For each IVET study, the selection strategy is specified. Most assignments of genes and gene product functions are based on similarity to known genes as described in the original papers. Some of these assignments were further verified or updated through homology searches with available gene sequences. Genes subsequently shown to be required for interaction with a host are indicated in bold. Abbreviations: ABC, ATP-binding cassette; CRP, cAMP receptor protein; gfp-LA, GFP-based IVET leaf array; IHF, integration host factor; MCP, methyl-accepting chemotaxis protein; PHB, polyhydroxybutyrate; PTS, phosphotransferase system; SRP, signal recognition particle; TRAP-T, tripartite ATP-independent periplasmic transporter; TTSS, type III secretion system. a, H. Rediers, unpublished results; b, M. S. Thomas, unpublished results.