Table 4.

Genes and operons of known function exhibiting decreased transcription in early postexponential-phase cells of SCV strain WN716

Category, subcategory, and gene or operonFunction(s)aFold expression decreaseb
Category 1. Cell envelope and cellular processes
    1.1 Cell wall
        lytAInvolved in secretion of major autolysin LytC7
        lytCN-Acetylmuramoyl-l-alanine amidase; major autolysin; involved in motility and cell separation9
        lytDN-Acetylglucosaminidase, major autolysin7
    1.2 Transport/binding proteins and lipoproteins
        Oligopeptide ABC transport system
            appDATP-binding protein4
            appFATP-binding protein6
            appASubstrate-binding protein10
            feuAIron transport substrate-binding protein11
            feuBIron transport permease (integral membrane protein)1
            feuCIron transport permease (integral membrane protein)20
        Glycine betaine/proline/choline transport
            opuBAATP-binding protein
            opuBCSubstrate-binding protein13
        Glycine betaine/carnitine/choline transport
            opuCAATP-binding protein7
            opuCCSubstrate-binding protein19
        Oligopeptide transport system (competence, sporulation initiation)
            oppASubstrate-binding protein6
            oppDATP-binding protein2
            oppFATP-binding protein10
    1.3 Sensors (signal transduction)
        cheBChemotaxis response regulator17
        cheAChemotaxis sensor kinase8
    1.4 Membrane bioenergetics (electron transport chain, ATP synthase
        Cytochrome caa3 oxidase
            ctaARequired for biosynthesis2
            ctaBAssembly factor3
            ctaCSubunit II6
            ctaDSubunit I1
            ctaESubunit III13
            ctaFSubunit IV2
            ctaGRequired for biosynthesis2
            resACytochrome c biogenesis protein, similar to thioredoxin12
            resBCytochrome c biogenesis protein4
            resCCytochrome c biogenesis protein4
    1.5 Motility and chemotaxis
        mcpBMethyl-accepting chemotaxis protein11
        tlpAMethyl-accepting chemotaxis protein432
        mcpAMethyl-accepting chemotaxis protein20
        flgBFlagellar basal body rod protein11
        flgCFlagellar basal body rod protein2
        fliEFlagellar hook-basal body complex protein19
        fliFFlagellar basal body M-ring protein12
        fliGFlagellar motor switch protein40
        fliHFlagellar assembly protein16
        fliIFlagellum-specific ATP synthase12
        fliJFlagellar protein required for basal body formation27
        fliKFlagellar hook-length control protein17
        flgEFlagellar hook protein15
        fliMFlagellar motor switch protein13
        fliYFlagellar motor switch protein28
        cheYChemotaxis response regulator15
        fliZProtein required for flagellum formation14
        fliPProtein required for flagellum formation25
        fliQProtein required for flagellum formation
        fliRProtein required for flagellum formation24
        flhBFlagellum-associated protein2
        flhAFlagellum-associated protein18
        flhFFlagellum-associated protein13
        ylxHSimilar to flagellar switch protein20
        cheWPurine-binding chemotaxis protein10
        cheCCheY-P phosphatase5
        cheDFlagellar motor switch protein8
        yvyFSimilar to flagellar protein6
        flgMAnti-sigma-D factor10
        yvyGSimilar to flagellar protein16
        flgKFlagellar hook-associated protein 110
        flgLFlagellar hook-associated protein 322
        yvyCSimilar to flagellar protein
        fliDFlagellar hook-associated protein 219
        fliSFlagellar protein12
        fliTFlagellar protein24
        flhOFlagellar basal body rod protein8
        flhPFlagellar hook-basal body protein9
    1.6 Protein secretion
        lytAMembrane-bound protein, secretion of LytC7
    1.8 Sporulation
        rapAResponse regulator aspartate phosphatase (Spo0F∼P)21
        phrARapA inhibitor22
        rapCResponse regulator aspartate phosphatase7
        phrCRapC inhibitor; competence and sporulation stimulating factor (CSF)17
        rapFResponse regulator aspartate phosphatase10
        phrFRapF inhibitor12
        cotWSpore coat protein (insoluble fraction)12
        spoIIDRequired for dissolution of asymmetric septum11
        spoIIABAnti-sigma factor serine kinase11
        spoVIDRequired for assembly of spore coat9.5
        sspFMinor α/β-type small acid-soluble spore protein44
    1.10 Transformation/competence
        comCLate competence protein15
        comSCompetence protein (embedded in srfAB)39
        comXCompetence pheromone precursor8
Category 2. Intermediary metabolism
    2.1 Metabolism of carbohydrates and related molecules
        2.1.1 Specific pathways
            alsSα-Acetolactate synthase, acetoin production122
            alsDα-Acetolactate decarboxylase, acetoin production87
            kdgRRepressor of kdg operon, LacI family1
            kdgK2-Keto-3-deoxygluconate kinase (pectin utilization)2
            kdgA2-Keto-3-deoxyphosphogluconate aldolase (pectin utilization)13
            kdgT2-Keto-3-deoxygluconate permease (pectin utilization)2
    2.2 Metabolism of amino acids and related molecules
        mprExtracellular metalloprotease8
    2.5 Metabolism of coenzymes and prosthetic groups
        bioW6-Carboxylhexanoate-CoA ligase5
        bioAAdoMet-8-amino-7-oxononanoate aminotransferase6
        bioF8-Amino-7-oxononanoate synthase4
        bioDDethiobiotin synthetase16
        bioBBiotin synthetase14
        bioIBiotin synthesis cytochrome P450-like enzyme19
Category 3. Information pathways
    3.1 DNA replication
        dnaAInitiation of chromosome replication13
        dnaNDNA polymerase III beta subunit7
    3.2 DNA restriction/modification and repair
        alkADNA-3-methyladenine glycosidase10
        adaAMethylphosphotriester-DNA alkyltransferase/transcriptional activator of adaAB operon2
        adaBO6-methylguanine-DNA methyltransferase8
Category 4. Other functions
    4.2 Detoxification
        mmrMethylenomycin A resistance protein17
    4.3 Antibiotic production
        pksDPolyketide synthesis148
        pksSPolyketide synthesis8.2
        srfAASurfactin synthetase subunit 117
        srfABSurfactin synthetase subunit 224
        srfACSurfactin synthetase subunit 324
        srfADSurfactin synthetase subunit 425
  • a AdoMet, S-adenosylmethionine.

  • b –, signal not detected.