TABLE 2.
Gene expression response of PA14 grown in the presence of tobramycin versus untreated control.
| Gene name | Gene ID | Gene product | RNA-seq | Ribo-seq |
| FC1 | FC | |||
| Energy metabolism and tricarboxylic acid cycle cycle | ||||
| PA14_06800 | PA14_06800 | Hypothetical protein | 18.422 | X3 |
| ldh | PA14_19870 | Leucine dehydrogenase | –13.38 | –2.23 |
| PA14_19900 | PA14_19900 | Pyruvate dehydrogenase E1 component subunit alpha | –104.77 | –4.45 |
| pdhB | PA14_19910 | Pyruvate dehydrogenase E1 component. beta chain | –94.26 | –2.53 |
| PA14_19920 | PA14_19920 | Branched-chain alpha-keto acid dehydrogenase subunit E2 | –78.9 | X |
| nqrA | PA14_25280 | Na(+)-translocating NADH-quinone reductase subunit A | 6.06 | ND4 |
| nqrB | PA14_25305 | Na(+)-translocating NADH-quinone reductase subunit B | ND | –4.6 |
| nqrC | PA14_25320 | Na(+)-translocating NADH-quinone reductase subunit C | –2.08 | –2.66 |
| nqrD | PA14_25330 | Na(+)-translocating NADH-quinone reductase subunit D | –5.14 | –3.25 |
| nqrE | PA14_25340 | Na(+)-translocating NADH-quinone reductase subunit E | –7.06 | –2.51 |
| nqrF | PA14_25350 | Na(+)-translocating NADH-quinone reductase subunit F | –9.6 | ND |
| nuoN | PA14_29850 | NADH dehydrogenase subunit N | –20.61 | –13.71 |
| nuoM | PA14_29860 | NADH dehydrogenase subunit M | –24.8 | –3.99 |
| nuoL | PA14_29880 | NADH dehydrogenase subunit L | –25.56 | –3.4 |
| nuoK | PA14_29890 | NADH dehydrogenase subunit K | –8 | –6.97 |
| nuoJ | PA14_29900 | NADH dehydrogenase subunit J | –5.16 | –15.98 |
| nuoI | PA14_29920 | NADH dehydrogenase subunit I | –9.55 | –13.6 |
| nuoH | PA14_29930 | NADH dehydrogenase subunit H | –10 | –4.88 |
| nuoG | PA14_29940 | NADH dehydrogenase subunit G | –46.39 | –8.11 |
| nuoF | PA14_29970 | NADH dehydrogenase I subunit F | –13.36 | –8.16 |
| nuoE | PA14_29980 | NADH dehydrogenase subunit E | –13.55 | –5.35 |
| icd | PA14_30190 | Iisocitrate dehydrogenase | –3.09 | ND |
| sucD | PA14_43940 | Succinyl-CoA synthetase subunit alpha | –9.39 | –3.27 |
| sucC | PA14_43950 | Succinyl-CoA synthetase subunit beta | –3.73 | ND |
| lpdG | PA14_43970 | Dihydrolipoamide dehydrogenase | –16.47 | –5.26 |
| sucB | PA14_44000 | Dihydrolipoamide succinyltransferase | –10.98 | –9.15 |
| sucA | PA14_44010 | 2-oxoglutarate dehydrogenase E1 | –4.27 | –4.12 |
| PA14_53970 | PA14_53970 | Aconitate hydratase | –18.05 | –8.09 |
| Phenylalanine/Tyrosine catabolism | ||||
| fahA | PA14_38530 | Fumarylacetoacetase | –30.98 | –2.32 |
| maiA | PA14_38550 | Maleylacetoacetate isomerase | –48.44 | –3.57 |
| phhB | PA14_53000 | Pterin-4-alpha-carbinolamine dehydratase | –14.76 | –2.47 |
| phhC | PA14_53010 | Aromatic amino acid aminotransferase | –13.94 | –2.78 |
| Arginine catabolism | ||||
| arcD | PA14_68300 | Arginine/ornithine antiporter | –49.29 | 2.29 |
| arcA | PA14_68330 | Arginine deiminase | –77.18 | –2.12 |
| arcB | PA14_68340 | Ornithine carbamoyltransferase | –137.35 | –4.19 |
| Leucin/Valine/Isoleucin degradation and biosynthesis | ||||
| lpdV | PA14_35490 | Dihydrolipoamide dehydrogenase | –104.5 | –6.56 |
| bkdB | PA14_35500 | Branched-chain alpha-keto acid dehydrogenase subunit E2 | –91.67 | –5.51 |
| bkdA2 | PA14_35520 | 2-oxoisovalerate dehydrogenase subunit beta | –104.31 | –4.84 |
| bkdA1 | PA14_35530 | 2-oxoisovalerate dehydrogenase subunit alpha | –5.23 | X |
| gnyR | PA14_38430 | Regulatory gene of gnyRDBHAL cluster. GnyR | –12.88 | ND |
| gnyD | PA14_38440 | Citronelloyl-CoA dehydrogenase. GnyD | –30.42 | –2.32 |
| gnyB | PA14_38460 | Acyl-CoA carboxyltransferase subunit beta | –27.71 | X |
| gnyH | PA14_38470 | Gamma-carboxygeranoyl-CoA hydratase | –33.85 | –3.73 |
| gnyA | PA14_38480 | Alpha subunit of geranoyl-CoA carboxylase. GnyA | –26.11 | X |
| ilvA2 | PA14_47100 | Threonine dehydratase | 24.7 | 7.68 |
| Peptidoglycan biosynthesis | ||||
| ddl | PA14_57320 | D-alanine–D-alanine ligase | –151.66 | –8.63 |
| murC | PA14_57330 | UDP-N-acetylmuramate–L-alanine ligase | –78.75 | –9.99 |
| murG | PA14_57340 | UDPdiphospho-muramoylpentapeptide beta-N-acetylglucosaminyl transferase | –44.2 | –8.27 |
| murD | PA14_57370 | UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase | –46.8 | –10.56 |
| mraY | PA14_57380 | Phospho-N-acetylmuramoyl-pentapeptide-transferase | –13.67 | –2.18 |
| murF | PA14_57390 | UDP-N-acetylmuramoylalanyl-D-glutamyl-2.6-diaminopimelate–D-alanyl-D-alanine ligase | –11.12 | X |
| murE | PA14_57410 | UDP-N-acetylmuramoylalanyl-D-glutamate–2. 6-diaminopimelate ligase | –55.53 | –9.29 |
| rmlC | PA14_68210 | dTDP-4-dehydrorhamnose 3.5-epimerase | –12.92 | –3.34 |
| Glycogen metabolism | ||||
| glgA | PA14_36570 | Glycogen synthase | –3.09 | –5.06 |
| PA14_36580 | PA14_36580 | Glycosyl hydrolase | –19.03 | –11.25 |
| PA14_36590 | PA14_36590 | 4-alpha-glucanotransferase | –34.5 | –21.54 |
| PA14_36605 | PA14_36605 | Maltooligosyl trehalose synthase | –27.97 | –10.78 |
| PA14_36620 | PA14_36620 | Hypothetical protein | –44.57 | –10.58 |
| PA14_36630 | PA14_36630 | Glycosyl hydrolase | –25.56 | –6.53 |
| glgB | PA14_36710 | Glycogen branching protein | –38.34 | –15.21 |
| PA14_36730 | PA14_36730 | Trehalose synthase | –30.78 | –16.68 |
| PA14_36740 | PA14_36740 | Hypothetical protein | –4.77 | –5.04 |
| glgP | PA14_36840 | Glycogen phosphorylase | –5.98 | –2.93 |
| PA14_36850 | PA14_36850 | Hypothetical protein | –2.26 | –2.9 |
| Pathogenicity and virulence | ||||
| tssL1 | PA14_00925 | Hypothetical protein | –17.71 | X |
| tssk1 | PA14_00940 | Hypothetical protein | –6.38 | –4.32 |
| tssJ1 | PA14_00960 | Lipoprotein | –12.26 | –3.67 |
| PA14_00960 | PA14_00970 | Hypothetical protein | –33.07 | –2.84 |
| pilJ | PA14_05360 | Twitching motility protein PilJ | –2.63 | ND |
| pilK | PA14_05380 | Methyltransferase PilK | –2.59 | ND |
| chpA | PA14_05390 | ChpA | –11.54 | –4.98 |
| PA14_05400 | PA14_05400 | Methylesterase | –20.38 | –3.72 |
| PA14_34000 | PA14_34000 | HsiH3 | –23.95 | –5.54 |
| stk1 | PA14_42880 | Stk1 | –2.19 | X |
| stp1 | PA14_42890 | Stp1 | –5.56 | –3.6 |
| PA14_42900 | PA14_42900 | IcmF2 | –3.59 | –2.57 |
| PA14_42910 | PA14_42910 | DotU2 | –11.99 | –3.08 |
| PA14_42920 | PA14_42920 | HsiJ2 | –7.75 | –3.42 |
| PA14_42940 | PA14_42940 | Lip2.2 | –20.14 | –3.56 |
| PA14_42950 | PA14_42950 | Fha2 | –25.63 | –5.86 |
| PA14_42960 | PA14_42960 | Lip2.2 | –77.39 | X |
| PA14_42970 | PA14_42970 | Sfa2 | –13.89 | –6.03 |
| PA14_42980 | PA14_42980 | ClpV2 | –10.86 | –5.68 |
| PA14_42990 | PA14_42990 | HsiH2 | –10.56 | –4.18 |
| PA14_43000 | PA14_43000 | HsiG2 | –14.05 | –3.6 |
| PA14_43020 | PA14_43020 | Hypothetical protein | –10.04 | –3.57 |
| PA14_43030 | PA14_43030 | HsiC2 | –4.85 | X |
| flhB | PA14_45720 | Flagellar biosynthesis protein FlhB | –5.62 | X |
| fliR | PA14_45740 | Flagellar biosynthesis protein FliR | –8.13 | X |
| fliQ | PA14_45760 | Flagellar biosynthesis protein FliQ | –10.6 | X |
| fliP | PA14_45770 | Flagellar biosynthesis protein FliP | –6.41 | X |
| fliN | PA14_45790 | Flagellar motor switch protein | –2.05 | X |
| flgK | PA14_50360 | Flagellar hook-associated protein FlgK | –75.19 | –3.47 |
| flgJ | PA14_50380 | Flagellar rod assembly protein/muramidase FlgJ | –9.17 | –4.58 |
| flgI | PA14_50410 | Flagellar basal body P-ring protein | –6.22 | X |
| flgH | PA14_50420 | Flagellar basal body L-ring protein | –3.99 | X |
| flgG | PA14_50430 | Flagellar basal body rod protein FlgG | ND | 2.13 |
| flgF | PA14_50440 | Flagellar basal body rod protein FlgF | ND | 3.54 |
| pqsE | PA14_51380 | Quinolone signal response protein | –80.7 | –2.98 |
| pqsD | PA14_51390 | 3-oxoacyl-ACP synthase | –90.01 | –5.86 |
| pqsC | PA14_51410 | PqsC | –44.86 | –4.06 |
| pqsB | PA14_51420 | PqsB | –20.71 | –2.34 |
| pqsA | PA14_51430 | PqsA | –3.73 | X |
| PA14_55780 | PA14_55780 | Phosphate transporter | –46.70 | X |
| PA14_55790 | PA14_55790 | Two-component sensor | –15.49 | –2.70 |
| PA14_55800 | PA14_55800 | Hypothetical protein | –2.21 | X |
| PA14_55810 | PA14_55810 | Hypothetical protein | –2.73 | –2.00 |
| PA14_55820 | PA14_55820 | Two-component response regulator | –25.16 | X |
| PA14_55840 | PA14_55840 | Hypothetical protein | –84.76 | X |
| PA14_55850 | PA14_55850 | Hypothetical protein | –68.52 | X |
| PA14_55860 | PA14_55860 | Pilus assembly protein | –98.84 | X |
| PA14_55880 | PA14_55880 | Hypothetical protein | –105.85 | X |
| cpaF2 | PA14_55890 | Hypothetical protein | –111.85 | X |
| PA14_55900 | PA14_55900 | Type II secretion system protein | –36.82 | –9.16 |
| PA14_55920 | PA14_55920 | Hypothetical protein | –15.84 | –2.00 |
| PA14_55930 | PA14_55930 | Type II secretion system protein | –2.75 | ND |
| PA14_55940 | PA14_55940 | Pilus assembly protein | –8.25 | –7.96 |
| pilC | PA14_58760 | Type 4 fimbrial biogenesis protein pilC | –2.41 | ND |
| pilD | PA14_58770 | Type 4 prepilin peptidase PilD | –11.48 | ND |
| coaE | PA14_58780 | Dephospho-CoA kinase | ND | 2.48 |
| fimU | PA14_60280 | Type 4 fimbrial biogenesis protein FimU | –2.46 | ND |
| pilW | PA14_60290 | Type 4 fimbrial biogenesis protein PilW | –11.99 | X |
| pilX | PA14_60300 | Type 4 fimbrial biogenesis protein PilX | –9.12 | X |
| pilY1 | PA14_60310 | Type 4 fimbrial biogenesis protein PilY1 | –4.06 | ND |
| pilE | PA14_60320 | Type 4 fimbrial biogenesis protein PilE | –3.43 | –2.53 |
| PA14_65520 | PA14_65520 | Hypothetical protein | –21.34 | –3.44 |
| PA14_65540 | PA14_65540 | Hypothetical protein | –4.26 | X |
| estA | PA14_67510 | Esterase EstA | –11.29 | –2.17 |
| ABC transporters and Sha antiporter | ||||
| opuCA | PA14_13580 | ABC transporter ATP-binding protein | –28.83 | –7.05 |
| opuCB | PA14_13590 | ABC transporter permease | –6 | –4.83 |
| opuCD | PA14_13600 | ABC transporter substrate-binding protein | –4.73 | –4.41 |
| nppA2 | PA14_41130 | ABC transporter substrate-binding protein NppA2 | –1.97 | X |
| nppB | PA14_41140 | Peptidyl nucleoside antibiotic ABC transporter permease NppB | –10.23 | X |
| nppC | PA14_41150 | Peptidyl nucleoside antibiotic ABC transporter permease NppC | –30.15 | –3.71 |
| nppD | PA14_41160 | Peptidyl nucleoside antibiotic ABC transporter ATP-binding protein NppD | –22.25 | –4.98 |
| fabI | PA14_41170 | NADH-dependent enoyl-ACP reductase | –21.89 | –5.27 |
| phaG | PA14_50680 | ShaA | –44.11 | –3.99 |
| phaF | PA14_50690 | ShaB | –29.33 | –3.77 |
| phaE | PA14_50700 | ShaC | –12.23 | –2.9 |
| phaD | PA14_50710 | ShaD | –7.08 | –5.88 |
| phaC | PA14_50720 | ShaE | –8.48 | –7.78 |
| dppC | PA14_58450 | Dipeptide ABC transporter permease DppC | –13.03 | –3.55 |
| dppD | PA14_58470 | Dipeptide ABC transporter ATP-binding protein DppD | –34.43 | –10.45 |
| dppF | PA14_58490 | Dipeptide ABC transporter ATP-binding protein DppF | –21.5 | –4.19 |
| Transcription and translation | ||||
| tufB | PA14_08680 | Elongation factor Tu | 92.01 | 3.09 |
| rplC | PA14_08850 | 50S ribosomal protein L3 | 27.97 | ND |
| rplD | PA14_08860 | 50S ribosomal protein L4 | 23.35 | 2.05 |
| tyrS | PA14_10420 | Tyrosyl-tRNA synthetase | 37.72 | 11.48 |
| orf2 | PA14_12350 | (dimethylallyl)adenosine tRNA methylthiotransferase | 23.15 | 2.17 |
| rimM | PA14_15980 | 16S rRNA-processing protein RimM | 55.59 | 5.82 |
| trmD | PA14_15990 | tRNA (guanine-N(1)-)-methyltransferase | 52.24 | 4.74 |
| rpsB | PA14_17060 | 30S ribosomal protein S2 | 106.77 | 2.27 |
| deaD | PA14_27370 | ATP-dependent RNA helicase | 122.76 | 2.02 |
| infC | PA14_28660 | Translation initiation factor IF-3 | 12.93 | 2.59 |
| yadB | PA14_62510 | Glutamyl-Q tRNA(Asp) synthetase | 34.45 | 4.5 |
| yhbC | PA14_62780 | Hypothetical protein | 14.37 | ND |
| smpB | PA14_63060 | SsrA-binding protein | 12.7 | 2.36 |
| rpmE | PA14_66710 | 50S ribosomal protein L31 | 316.32 | ND |
| prfH | PA14_72200 | Peptide chain release factor-like protein | 491.76 | 5.65 |
| rnpA | PA14_73420 | Ribonuclease P | 164.46 | 16.33 |
| Stringent response and toxin-antitoxin systems | ||||
| PA14_01510 | PA14_01510 | Hypothetical protein | 25.78 | 4.87 |
| PA14_01520 | PA14_01520 | Hypothetical protein | 28.84 | 4.71 |
| ndk | PA14_14820 | Nucleoside diphosphate kinase | 6.47 | ND |
| obgE | PA14_60445 | GTPase ObgE | 15.46 | 2.42 |
| vapI | PA14_61840 | Antitoxin HigA | 9.67 | 5.8 |
| rnk | PA14_69630 | Nucleoside diphosphate kinase regulator | 11.23 | 2.08 |
| spoT | PA14_70470 | Guanosine-3′.5′-bis(diphosphate) 3′-pyrophosphohydrolase | 9.2 | 3.64 |
1FC, fold-change, p-value ≤ 0.05. 2Genes with FC ≤ –10 or ≥10 are represented in bold. 3X, not efficiently translated in the control and antibiotic treated samples, Ribo-seq BaseMean ≤ 50. 4ND, not differentially expressed, –2 ≤ FC ≤ 2 and/or p-value ≥ 0.05.