TABLE 2.

Differential gene expression in selected genes in ST (MJK3, MJK8, MJK22, and MJK123) compared to WT (PAO1)

Gene type and no.aDescriptionbFold geometric mean change (×/÷geometric SD)c
Bacteriophage
    PA0717Hypothetical protein of bacteriophage Pf1−70.4 (1.3)
    PA0718Hypothetical protein of bacteriophage Pf1−65.7 (1.4)
    PA0719Hypothetical protein of bacteriophage Pf1−102.2 (1.4)
    PA0720Helix-destabilizing protein of bacteriophage Pf1−48.1 (1.4)
    PA0721Hypothetical protein of bacteriophage Pf1−220.9 (1.9)
    PA0722Hypothetical protein of bacteriophage Pf1−65.7 (1.3)
    PA0723coaB, coat protein B of bacteriophage Pf1−40.1 (1.2)
    PA0724Probable coat protein A of bacteriophage Pf1−176.4 (1.5)
    PA0725Hypothetical protein of bacteriophage Pf1−104.0 (1.6)
    PA0726Hypothetical protein of bacteriophage Pf1−58.7 (1.1)
    PA0727Hypothetical protein of bacteriophage Pf1−49.4 (1.3)
    PA0728Probable bacteriophage integrase−122.6 (1.9)
Cell wall, LPS, capsule
    PA0763mucA, anti-sigma factor MucA−1.7 (1.1)
    PA0764mucB, negative regulator for alginate biosynthesis MucB−3.1 (1.2)
    PA0765mucC, positive regulator for alginate biosynthesis MucC−4.1 (1.3)
    PA0766dmucD, serine protease MucD precursor−1.3 (1.2)
    PA3387rhlG, beta-ketoacyl reductase−12.9 (1.6)
Flagellar motility
    PA1100fliE, flagellar hook-basal body complex protein FliE−4.4 (1.3)
    PA1101fliF, flagellar M-ring outer membrane protein precursor−3.0 (1.3)
    PA1102fliG, flagellar motor switch protein FliG−3.0 (1.4)
    PA1103fliH, probable flagellar assembly protein−2.2 (1.2)
    PA1104fliI, flagellum-specific ATP synthase FliI−2.3 (1.1)
    PA1105fliJ, flagellar protein FliJ−4.8 (1.4)
    PA1443fliM, flagellar motor switch protein FliM−2.1 (1.2)
    PA1444fliN, flagellar motor switch protein FliN−1.9 (1.2)
    PA1445fliO, flagellar protein FliO−2.7 (1.3)
    PA1446fliP, flagellar biosynthesis protein FliP−2.0 (1.2)
    PA1447fliQ, flagellar biosynthesis protein FliQ−1.8 (1.2)
    PA1448fliR, flagellar biosynthesis protein FliR−2.0 (1.1)
    PA1449flhB, flagellar biosynthesis protein FlhB−1.9 (1.3)
    PA1452flhA, flagellar biosynthesis protein FlhA−6.3 (1.5)
    PA1453flhF, flagellar biosynthesis protein FlhF−2.7 (1.3)
Denitrification
    PA0516nirF, heme d1 biosynthesis protein NirF3.3 (1.4)
    PA0517nirC, probable cytochrome c-type precursor3.2 (1.4)
    PA0518nirM, cytochrome c-551 precursor5.1 (1.4)
    PA0519nirS, nitrate reductase precursor4.0 (1.3)
    PA0520nirQ, regulatory protein NirQ2.4 (1.3)
    PA0521nirO, probable cytochrome c oxidase subunitNone
    PA0522nirP, hypothetical proteinNone
    PA0523norC, nitric oxide reductase subunit C8.4 (1.4)
    PA0524norB, nitric oxide reductase subunit B6.9 (1.4)
    PA0525norD, probable denitrification protein NorD16.0 (1.7)
    PA1172dnapC, cytochrome c-type protein NapC4.7 (1.6)
    PA1173dnapB, cytochrome c-type protein NapB precursor4.7 (1.7)
    PA1174napA, periplasmic nitrate reductase protein NapA7.1 (1.4)
    PA1175dnapD, periplasmic nitrate reductase protein NapD5.2 (1.6)
    PA1176dnapF, ferrodoxin protein NapF4.8 (1.6)
    PA1177dnapE, periplasmic nitrate reductase protein NapE8.1 (2.1)
    PA4133cytN, cytochrome c oxidase subunit (cbb3 type)18.1 (3.0)
Putative EPS biosynthesis
    PA2231pslA, probable glycosyl transferaseNone
    PA2232pslB, probable phosphomannose isomerase/GDP-mannose pyrophosphorylase2.6 (1.3)
    PA2233dpslC, probable glycosyl transferase2.4 (1.4)
    PA2234pslD, probable exopolysaccharide transporter2.7 (1.3)
    PA2235dpslE, hypothetical protein2.1 (1.2)
    PA2236dpslF, hypothetical protein2.2 (1.2)
    PA2237dpslG, probable glycosyl hydrolase2.3 (1.4)
    PA2238dpslH, hypothetical protein2.4 (1.2)
    PA2239dpslI, probable transferase2.0 (1.2)
    PA2240dpslJ, hypothetical protein2.1 (1.2)
    PA2241pslK, hypothetical proteinNone
    PA2242dpslL, hypothetical protein1.7 (1.1)
    PA2243pslM, hypothetical proteinNone/decrease
    PA2244pslN, hypothetical proteinNone
    PA2245pslO, hypothetical proteinNone/decrease
    PA3058dpelG, hypothetical protein2.9 (1.5)
    PA3059pelF, hypothetical protein4.5 (1.4)
    PA3060pelE, hypothetical protein9.1 (2.1)
    PA3061pelD, hypothetical protein6.4 (1.2)
    PA3062pelC, hypothetical protein9.4 (1.2)
    PA3063dpelB, hypothetical protein3.6 (1.3)
    PA3064dpelA, hypothetical protein4.9 (2.2)
Type IV pilus function
    PA0395pilT, twitching motility protein PilTNone
    PA0396dpilU, twitching motility protein PilU2.1 (1.2)
    PA0408dpilG, twitching motility protein PilG1.5 (1.1)
    PA0409dpilH, twitching motility protein PilH1.8 (1.2)
    PA0410dpilI, twitching motility protein PilI1.9 (1.1)
    PA0411dpilJ, twitching motility protein PilJ2.3 (1.3)
    PA0412dpilK, methyltransferase PilK2.0 (1.1)
    PA4525pilA, type IV fimbrial precursor PilA2.7 (1.3)
    PA4526dpilB, type IV fimbrial biogenesis protein PilB2.0 (1.3)
    PA4527pilC, still frameshift type IV fimbrial biogenesis protein PilCNone
    PA4528dpilD, type IV prepilin peptidase PilD1.6 (1.0)
    PA4551pilV, type IV fimbrial biogenesis protein PilVNone
    PA4552dpilW, type IV fimbrial biogenesis protein PilW1.9 (1.2)
    PA4553dpilX, type IV fimbrial biogenesis protein PilX2.3 (1.2)
    PA4554dpilY1, type IV fimbrial biogenesis protein PilY11.9 (1.1)
    PA4555pilY2, type IV fimbrial biogenesis protein PilY22.5 (1.2)
    PA4556pilE, type IV fimbrial biogenesis protein PilE2.3 (1.5)
    PA5040pilQ, type IV fimbrial biogenesis protein outer membrane protein PilQ precursor2.1 (1.2)
    PA5041pilP, type IV fimbrial biogenesis protein PilP1.8 (1.1)
    PA5042pilO, type IV fimbrial biogenesis protein PilO1.7 (1.1)
    PA5043dpilN, type IV fimbrial biogenesis protein PilN1.7 (1.0)
    PA5044pilM, type IV fimbrial biogenesis protein PilMNone
Quorum sensing controlled
    PA1430dlasR, transcriptional regulator LasR2.4 (1.3)
    PA1431rsaL, regulatory protein RsaL9.8 (1.5)
    PA1871dlasA, protease precursor LasA13.9 (2.3)
    PA2193hcnA, hydrogen cyanide synthase HcnA13.7 (2.4)
    PA2194hcnB, hydrogen cyanide synthase HcnB9.0 (2.1)
    PA2195hcnC, hydrogen cyanide synthase HcnC19.5 (2.4)
    PA3476rhlI, autoinducer synthesis protein RhlI3.6 (1.5)
    PA3477drhlR, transcriptional regulator RhlR3.4 (1.2)
    PA3478drhlB, rhamnosyltransferase chain B5.3 (1.5)
    PA3479drhlA, rhamnosyltransferase chain A7.6 (1.5)
    PA3724dlasB, elastase LasB76.1 (1.8)
  • a Gene numbers are from the Pseudomonas genome project (www.pseudomonas.com).

  • b Protein descriptions are from the Pseudomonas genome project (18).

  • c Negative change means that the genes were down-regulated in ST compared to WT. Positive change means that the genes were up-regulated in ST compared to WT.

  • d Fewer than 8 of 8 comparisons were up-regulated or down-regulated.