TABLE 2.
Differential gene expression in selected genes in ST (MJK3, MJK8, MJK22, and MJK123) compared to WT (PAO1)
| Gene type and no.a | Descriptionb | Fold geometric mean change (×/÷geometric SD)c |
|---|---|---|
| Bacteriophage | ||
| PA0717 | Hypothetical protein of bacteriophage Pf1 | −70.4 (1.3) |
| PA0718 | Hypothetical protein of bacteriophage Pf1 | −65.7 (1.4) |
| PA0719 | Hypothetical protein of bacteriophage Pf1 | −102.2 (1.4) |
| PA0720 | Helix-destabilizing protein of bacteriophage Pf1 | −48.1 (1.4) |
| PA0721 | Hypothetical protein of bacteriophage Pf1 | −220.9 (1.9) |
| PA0722 | Hypothetical protein of bacteriophage Pf1 | −65.7 (1.3) |
| PA0723 | coaB, coat protein B of bacteriophage Pf1 | −40.1 (1.2) |
| PA0724 | Probable coat protein A of bacteriophage Pf1 | −176.4 (1.5) |
| PA0725 | Hypothetical protein of bacteriophage Pf1 | −104.0 (1.6) |
| PA0726 | Hypothetical protein of bacteriophage Pf1 | −58.7 (1.1) |
| PA0727 | Hypothetical protein of bacteriophage Pf1 | −49.4 (1.3) |
| PA0728 | Probable bacteriophage integrase | −122.6 (1.9) |
| Cell wall, LPS, capsule | ||
| PA0763 | mucA, anti-sigma factor MucA | −1.7 (1.1) |
| PA0764 | mucB, negative regulator for alginate biosynthesis MucB | −3.1 (1.2) |
| PA0765 | mucC, positive regulator for alginate biosynthesis MucC | −4.1 (1.3) |
| PA0766d | mucD, serine protease MucD precursor | −1.3 (1.2) |
| PA3387 | rhlG, beta-ketoacyl reductase | −12.9 (1.6) |
| Flagellar motility | ||
| PA1100 | fliE, flagellar hook-basal body complex protein FliE | −4.4 (1.3) |
| PA1101 | fliF, flagellar M-ring outer membrane protein precursor | −3.0 (1.3) |
| PA1102 | fliG, flagellar motor switch protein FliG | −3.0 (1.4) |
| PA1103 | fliH, probable flagellar assembly protein | −2.2 (1.2) |
| PA1104 | fliI, flagellum-specific ATP synthase FliI | −2.3 (1.1) |
| PA1105 | fliJ, flagellar protein FliJ | −4.8 (1.4) |
| PA1443 | fliM, flagellar motor switch protein FliM | −2.1 (1.2) |
| PA1444 | fliN, flagellar motor switch protein FliN | −1.9 (1.2) |
| PA1445 | fliO, flagellar protein FliO | −2.7 (1.3) |
| PA1446 | fliP, flagellar biosynthesis protein FliP | −2.0 (1.2) |
| PA1447 | fliQ, flagellar biosynthesis protein FliQ | −1.8 (1.2) |
| PA1448 | fliR, flagellar biosynthesis protein FliR | −2.0 (1.1) |
| PA1449 | flhB, flagellar biosynthesis protein FlhB | −1.9 (1.3) |
| PA1452 | flhA, flagellar biosynthesis protein FlhA | −6.3 (1.5) |
| PA1453 | flhF, flagellar biosynthesis protein FlhF | −2.7 (1.3) |
| Denitrification | ||
| PA0516 | nirF, heme d1 biosynthesis protein NirF | 3.3 (1.4) |
| PA0517 | nirC, probable cytochrome c-type precursor | 3.2 (1.4) |
| PA0518 | nirM, cytochrome c-551 precursor | 5.1 (1.4) |
| PA0519 | nirS, nitrate reductase precursor | 4.0 (1.3) |
| PA0520 | nirQ, regulatory protein NirQ | 2.4 (1.3) |
| PA0521 | nirO, probable cytochrome c oxidase subunit | None |
| PA0522 | nirP, hypothetical protein | None |
| PA0523 | norC, nitric oxide reductase subunit C | 8.4 (1.4) |
| PA0524 | norB, nitric oxide reductase subunit B | 6.9 (1.4) |
| PA0525 | norD, probable denitrification protein NorD | 16.0 (1.7) |
| PA1172d | napC, cytochrome c-type protein NapC | 4.7 (1.6) |
| PA1173d | napB, cytochrome c-type protein NapB precursor | 4.7 (1.7) |
| PA1174 | napA, periplasmic nitrate reductase protein NapA | 7.1 (1.4) |
| PA1175d | napD, periplasmic nitrate reductase protein NapD | 5.2 (1.6) |
| PA1176d | napF, ferrodoxin protein NapF | 4.8 (1.6) |
| PA1177d | napE, periplasmic nitrate reductase protein NapE | 8.1 (2.1) |
| PA4133 | cytN, cytochrome c oxidase subunit (cbb3 type) | 18.1 (3.0) |
| Putative EPS biosynthesis | ||
| PA2231 | pslA, probable glycosyl transferase | None |
| PA2232 | pslB, probable phosphomannose isomerase/GDP-mannose pyrophosphorylase | 2.6 (1.3) |
| PA2233d | pslC, probable glycosyl transferase | 2.4 (1.4) |
| PA2234 | pslD, probable exopolysaccharide transporter | 2.7 (1.3) |
| PA2235d | pslE, hypothetical protein | 2.1 (1.2) |
| PA2236d | pslF, hypothetical protein | 2.2 (1.2) |
| PA2237d | pslG, probable glycosyl hydrolase | 2.3 (1.4) |
| PA2238d | pslH, hypothetical protein | 2.4 (1.2) |
| PA2239d | pslI, probable transferase | 2.0 (1.2) |
| PA2240d | pslJ, hypothetical protein | 2.1 (1.2) |
| PA2241 | pslK, hypothetical protein | None |
| PA2242d | pslL, hypothetical protein | 1.7 (1.1) |
| PA2243 | pslM, hypothetical protein | None/decrease |
| PA2244 | pslN, hypothetical protein | None |
| PA2245 | pslO, hypothetical protein | None/decrease |
| PA3058d | pelG, hypothetical protein | 2.9 (1.5) |
| PA3059 | pelF, hypothetical protein | 4.5 (1.4) |
| PA3060 | pelE, hypothetical protein | 9.1 (2.1) |
| PA3061 | pelD, hypothetical protein | 6.4 (1.2) |
| PA3062 | pelC, hypothetical protein | 9.4 (1.2) |
| PA3063d | pelB, hypothetical protein | 3.6 (1.3) |
| PA3064d | pelA, hypothetical protein | 4.9 (2.2) |
| Type IV pilus function | ||
| PA0395 | pilT, twitching motility protein PilT | None |
| PA0396d | pilU, twitching motility protein PilU | 2.1 (1.2) |
| PA0408d | pilG, twitching motility protein PilG | 1.5 (1.1) |
| PA0409d | pilH, twitching motility protein PilH | 1.8 (1.2) |
| PA0410d | pilI, twitching motility protein PilI | 1.9 (1.1) |
| PA0411d | pilJ, twitching motility protein PilJ | 2.3 (1.3) |
| PA0412d | pilK, methyltransferase PilK | 2.0 (1.1) |
| PA4525 | pilA, type IV fimbrial precursor PilA | 2.7 (1.3) |
| PA4526d | pilB, type IV fimbrial biogenesis protein PilB | 2.0 (1.3) |
| PA4527 | pilC, still frameshift type IV fimbrial biogenesis protein PilC | None |
| PA4528d | pilD, type IV prepilin peptidase PilD | 1.6 (1.0) |
| PA4551 | pilV, type IV fimbrial biogenesis protein PilV | None |
| PA4552d | pilW, type IV fimbrial biogenesis protein PilW | 1.9 (1.2) |
| PA4553d | pilX, type IV fimbrial biogenesis protein PilX | 2.3 (1.2) |
| PA4554d | pilY1, type IV fimbrial biogenesis protein PilY1 | 1.9 (1.1) |
| PA4555 | pilY2, type IV fimbrial biogenesis protein PilY2 | 2.5 (1.2) |
| PA4556 | pilE, type IV fimbrial biogenesis protein PilE | 2.3 (1.5) |
| PA5040 | pilQ, type IV fimbrial biogenesis protein outer membrane protein PilQ precursor | 2.1 (1.2) |
| PA5041 | pilP, type IV fimbrial biogenesis protein PilP | 1.8 (1.1) |
| PA5042 | pilO, type IV fimbrial biogenesis protein PilO | 1.7 (1.1) |
| PA5043d | pilN, type IV fimbrial biogenesis protein PilN | 1.7 (1.0) |
| PA5044 | pilM, type IV fimbrial biogenesis protein PilM | None |
| Quorum sensing controlled | ||
| PA1430d | lasR, transcriptional regulator LasR | 2.4 (1.3) |
| PA1431 | rsaL, regulatory protein RsaL | 9.8 (1.5) |
| PA1871d | lasA, protease precursor LasA | 13.9 (2.3) |
| PA2193 | hcnA, hydrogen cyanide synthase HcnA | 13.7 (2.4) |
| PA2194 | hcnB, hydrogen cyanide synthase HcnB | 9.0 (2.1) |
| PA2195 | hcnC, hydrogen cyanide synthase HcnC | 19.5 (2.4) |
| PA3476 | rhlI, autoinducer synthesis protein RhlI | 3.6 (1.5) |
| PA3477d | rhlR, transcriptional regulator RhlR | 3.4 (1.2) |
| PA3478d | rhlB, rhamnosyltransferase chain B | 5.3 (1.5) |
| PA3479d | rhlA, rhamnosyltransferase chain A | 7.6 (1.5) |
| PA3724d | lasB, elastase LasB | 76.1 (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.