Table 5 Differentially expressed genes (> 1.0 and < − 1.0 log2FC and FDR ≤ 0.05) at 1 h induced by the polymyxin B/rifampicin combination
Gene name/locus tag | Product description | Expression ratio (log2) | Adjusted P-value |
|---|---|---|---|
Virulence factor | |||
phzA2, phzB2, phzC2, phzD2, phzE2, phzF2, phzG2, phzA1, phzB1, phzC1, phzG1, phzS, phzH, phzM | Phenazine biosynthesis protein | ≤ − 2.43 to − 5.01 | ≤ 0.001 |
flp | Type IV b pilin Flp | − 4.33 | 3.14E−06 |
xcpZ, xcpY, xcpX, xcpW, xcpV, xcpU, xcpT, xcpS, xcpR, xcpP, xcpQ | Type II secretion system protein | < − 1.15 to − 2.03 | ≤ 0.001 |
pslA, pslB, pslC, pslD, pslE, pslF, pslG, pslH, pslI, pslJ, pslK | Biofilm formation protein | < − 1.21 to − 2.09 | ≤ 0.001 |
pilV, pilW, pilY1, pilY2, pilE | Type IV fimbrial biogenesis protein | < − 1.04 to − 1.28 | ≤ 0.001 |
PA5265 | Hypothetical protein | − 2.84 | 5.08E−06 |
vgrG6 | Type VI secretion system, RhsGE-associated Vgr family subset | − 4.36 | 5.46E−07 |
hcpB | Secreted protein Hcp | − 4.55 | 5.20E−07 |
Antibiotic resistance | |||
oprB | Porin B | − 1.92 | 0.0005 |
oprD | Porin D | − 1.07 | 0.006 |
mexY | RND multidrug efflux | 2.60 | 3.92E−08 |
mexX | 2.85 | 9.59E−07 | |
Quorum sensing system | |||
lasA | Protease LasA | − 1.47 | 5.01E−06 |
lasB | Elastase LasB | − 2.99 | 3.65E−07 |
lasI | Acyl-homoserine-lactone synthase | 1.12 | 5.35E−06 |
rhlI | Acyl-homoserine-lactone synthase | − 1.33 | 1.08E−06 |
rhlR | Transcriptional regulator RhlR | − 1.98 | 7.03E−07 |
rhlB | Rhamnosyltransferase subunit B | − 3.15 | 3.98E−08 |
rhlA | Rhamnosyltransferase subunit A | − 3.53 | 3.93E−08 |
pqsA | Anthranilate–CoA ligase | − 1.92 | 4.37E−07 |
pqsB | Hypothetical protein | − 1.87 | 7.61E−08 |
pqsC | Hypothetical protein | − 1.76 | 3.29E−07 |
pqsD | 3-Oxoacyl-ACP synthase | − 1.66 | 4.03E−07 |
pqsE | Thioesterase PqsE | − 1.75 | 5.62E−07 |
pqsH | 2-Heptyl-3-hydroxy-4(1H)-quinolone synthase | − 1.49 | 7.21E−08 |
narI, narJ, narH, narG | Respiratory nitrate reductase subunit gamma | > 2.16 to 2.64 | < 0.05 |
narK2 | Nitrite extrusion protein | 3.11 | < 0.05 |
narK1 | Nitrite extrusion protein | 3.18 | < 0.05 |
nirN | Cytochrome C | − 2.51 | 2.24E−07 |
PA0510 | Uroporphyrin-III C-methyltransferase | − 2.99 | 3.93E−08 |
nirJ, nirH, nirG, nirL, nirD, nirF | Heme d1 biosynthesis protein | < 1.95 to − 3.15 | ≤ 0.001 |
nirC | Cytochrome c55X | − 2.26 | 5.33E−06 |
nirM | Cytochrome C-551 | − 2.65 | 1.68E−06 |
nirS | Nitrite reductase | − 2.94 | 5.35E−06 |
norB | Nitric oxide reductase subunit B | − 2.48 | 0.00031 |
norC | Nitric oxide reductase subunit B | − 2.42 | 0.00061 |
PA0525 | Denitrification protein NorD | − 2.30 | 0.00027 |
nosR | Regulatory protein NosR | − 1.93 | 1.80E−05 |
nosZ | Nitrous-oxide reductase | − 1.89 | 5.23E−07 |
nosD | Copper-binding periplasmic protein | − 2.13 | 1.94E−07 |
nosF | Copper ABC transporter ATP-binding protein | − 2.47 | 1.24E−05 |
nosY | Membrane protein NosY | − 2.51 | 3.86E−08 |
nosL | Accessory protein NosL | − 2.03 | 4.46E−06 |
Central carbon metabolism/respiration | |||
PA3928 | Hypothetical protein | − 2.86 | 2.67E−06 |
cioB | Cyanide insensitive terminal oxidase | − 3.20 | 5.23E−07 |
cioA | Cyanide insensitive terminal oxidase | − 3.43 | 7.44E−07 |
PA0521 | Cytochrome C oxidase subunit | − 2.24 | 0.000649 |
PA4133 | cbb3-type cytochrome C oxidase subunit I | − 2.59 | 1.24E−05 |
RpoS | RNA polymerase sigma factor RpoS | − 1.31 | 6.61E−06 |