Table 1.
The core biofilm transcriptome.
| Upregulated genes | Downregulated genes | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Locus tag | Gene | Log 2 FC | Locus tag | Gene | Log 2 FC | Locus tag | Gene | Log 2 FC | |||
| PA14 | PAO1 | PA14 | PAO1 | PA14 | PAO1 | ||||||
| PA14_06090 | PA0466 | 2.9 | PA14_38850 | PA1983 | exaB | 6.8 | PA14_04650 | PA0355 | pfpI | −3.2 | |
| PA14_06180 | PA0472 | fiuI | 2.5 | PA14_38860 | PA1982 | exaA | 5.8 | PA14_06650 | PA0509 | nirN | −3.0 |
| PA14_07355 | PA0565 | 3.6 | PA14_38880 | PA1981 | 5.7 | PA14_06660 | PA0510 | nirE | −3.3 | ||
| PA14_09980 | PA4167 | dkgB | 2.7 | PA14_38900 | PA1980 | exaE | 2.9 | PA14_06670 | PA0511 | nirJ | −3.5 |
| PA14_10170 | PA4159 | fepB | 3.2 | PA14_38910 | PA1979 | exaD | 3.0 | PA14_06680 | PA0512 | nirH | −3.2 |
| PA14_10200 | PA4156 | 2.8 | PA14_38920 | — | 4.1 | PA14_06690 | PA0513 | nirG | −2.9 | ||
| PA14_10240 | PA4152 | acoC | 2.8 | PA14_38970 | PA1976 | 2.9 | PA14_06700 | PA0514 | nirL | −3.3 | |
| PA14_10250 | PA4151 | acoB | 3.0 | PA14_38990 | PA1975 | 3.1 | PA14_06710 | PA0515 | nirD | −3.3 | |
| PA14_10260 | PA4150 | acoA | 3.1 | PA14_39000 | PA1974 | 4.9 | PA14_06720 | PA0516 | nirF | −3.1 | |
| PA14_10270 | PA4149 | acoX | 3.5 | PA14_39050 | PA1971 | braZ | 2.5 | PA14_06730 | PA0517 | nirC | −3.9 |
| PA14_10280 | PA4148 | 3.6 | PA14_39260 | PA1952 | 2.7 | PA14_06740 | PA0518 | nirM | −4.8 | ||
| PA14_10400 | — | 3.2 | PA14_39590 | PA1927 | metE | 4.3 | PA14_06750 | PA0519 | nirS | −4.9 | |
| PA14_10410 | — | 2.9 | PA14_39720 | PA1918 | 2.6 | PA14_06770 | PA0520 | nirQ | −3.3 | ||
| PA14_11070 | PA4085 | cupB2 | 2.7 | PA14_39750 | PA1916 | 2.7 | PA14_06810 | PA0523 | norC | −5.9 | |
| PA14_19270 | PA3467 | 2.7 | PA14_39860 | PA1907 | 2.5 | PA14_06830 | PA0524 | norB | −4.5 | ||
| PA14_20010 | PA3408 | hasR | 3.3 | PA14_39980 | PA1898 | qscR | 2.6 | PA14_06840 | PA0525 | norD | −4.4 |
| PA14_20020 | PA3407 | hasAp | 5.1 | PA14_40040 | PA1893 | 2.7 | PA14_06860 | PA0526 | −3.9 | ||
| PA14_20030 | PA3406 | hasD | 3.1 | PA14_40050 | PA1892 | 2.7 | PA14_09610 | PA4200 | −2.5 | ||
| PA14_20040 | PA3405 | hasE | 3.0 | PA14_40060 | PA1891 | 3.0 | PA14_09660 | PA4198 | −2.6 | ||
| PA14_20050 | PA3404 | hasF | 2.7 | PA14_40270 | PA1873 | 2.8 | PA14_16640 | PA3691 | −2.9 | ||
| PA14_21530 | PA3287 | 3.1 | PA14_40520 | PA1855 | 2.7 | PA14_20180 | PA3394 | nosF | −2.8 | ||
| PA14_22320 | PA3237 | 4.0 | PA14_41510 | PA1783 | nasA | 2.8 | PA14_20190 | PA3393 | nosD | −2.8 | |
| PA14_27370 | PA2840 | deaD | 2.4 | PA14_41520 | PA1782 | ppkB | 2.6 | PA14_20200 | PA3392 | nosZ | −4.8 |
| PA14_28100 | PA2783 | 2.6 | PA14_41530 | PA1781 | nirB | 2.7 | PA14_20230 | PA3391 | nosR | −4.3 | |
| PA14_28360 | — | 2.7 | PA14_44190 | PA1569 | 2.8 | PA14_29640 | PA2664 | fhp | −3.8 | ||
| PA14_28620 | PA2746 | 3.2 | PA14_44520 | PA1541 | ydgF | 3.3 | PA14_29660 | PA2662 | −2.6 | ||
| PA14_29350 | PA2688 | pfeA | 2.6 | PA14_44530 | PA1540 | ygdE | 2.8 | PA14_40850 | PA1831 | gpmA | −2.4 |
| PA14_29480 | PA2678 | wzm | 2.7 | PA14_46850 | PA1347 | 2.8 | PA14_50520 | PA1074 | braC | −2.5 | |
| PA14_32080 | PA2518 | xylX | 3.3 | PA14_47380 | PA1302 | hxuC | 2.6 | PA14_52660 | PA0899 | aruB | −2.3 |
| PA14_32100 | PA2517 | xylY | 2.9 | PA14_47390 | PA1301 | 3.0 | PA14_52670 | PA0898 | astD | −2.2 | |
| PA14_33250 | PA2427 | 4.4 | PA14_47400 | PA1300 | 2.8 | PA14_52690 | PA0897 | aruG | −3.0 | ||
| PA14_33260 | PA2426 | pvdS | 3.0 | PA14_49690 | PA1137 | 3.8 | PA14_52720 | PA0895 | argD | −2.4 | |
| PA14_33270 | PA2425 | pvdG | 4.0 | PA14_50050 | PA1108 | 2.6 | PA14_56370 | PA4336 | −2.9 | ||
| PA14_33280 | PA2424 | pvdL | 3.8 | PA14_51460 | PA0993 | cupC2 | 3.2 | PA14_56780 | PA4366 | sodB | −2.6 |
| PA14_33500 | PA2413 | pvdH | 3.0 | PA14_52960 | PA0874 | 2.7 | PA14_57020 | PA4386 | groES | −2.7 | |
| PA14_33510 | PA2412 | 3.5 | PA14_53300 | PA0848 | 3.4 | PA14_60570 | PA4578 | −2.9 | |||
| PA14_33520 | PA2411 | 3.7 | PA14_55500 | PA0680 | hxcV | 2.6 | PA14_61650 | PA4661 | pagL | −2.7 | |
| PA14_33600 | PA2403 | fpvG | 3.1 | PA14_56770 | PA4365 | 2.5 | PA14_64480 | PA4876 | osmE | −2.7 | |
| PA14_33610 | PA2400 | 2.9 | PA14_57990 | PA4467 | 3.1 | PA14_64520 | PA4880 | −2.9 | |||
| PA14_33690 | PA2397 | pvdE | 3.3 | PA14_58000 | PA4468 | sodM | 3.1 | PA14_69770 | PA5285 | −2.6 | |
| PA14_33710 | PA2395 | pvdO | 3.0 | PA14_58010 | PA4469 | 3.5 | |||||
| PA14_33720 | PA2394 | pvdN | 3.2 | PA14_58030 | PA4470 | fumC | 3.3 | ||||
| PA14_33730 | PA2393 | 3.6 | PA14_58040 | PA4471 | 3.9 | ||||||
| PA14_33810 | PA2386 | pvdA | 4.5 | PA14_60480 | PA4570 | 4.1 | |||||
| PA14_33820 | PA2385 | pvdQ | 3.3 | PA14_68430 | PA5180 | fdhD | 2.9 | ||||
| PA14_35430 | PA2254 | pvcA | 2.7 | PA14_68440 | PA5181 | 2.5 | |||||
| PA14_35460 | PA2252 | 2.9 | PA2958.1 | PA2958.1 | rgsA | 3.7 | |||||
| PA14_35980 | — | 2.9 | PA3964-PA3965 | PA3964-PA3965 | P24 | 3.6 | |||||
| PA14_37380 | PA2097 | 2.4 | PA4704.1 | PA4704.1 | prrF1 | 3.3 | |||||
| PA14_38210 | PA2034 | 2.6 | PA4704.2 | PA4704.2 | prrF2 | 2.8 | |||||
| PA14_38220 | PA2033 | 2.6 | PA4704-PA4705 | PA4704-PA4705 | prrH | 3.1 | |||||
| PA14_38310 | PA2027 | 3.3 | |||||||||
The analysis of differentially expressed genes between transcriptional profiles of 77 clinical P. aeruginosa isolates recorded under static biofilm (BF) and planktonic (PL) growth conditions resulted in the identification of 143 genes. 103 genes were significantly upregulated; 40 genes were significantly downregulated (threshold: log 2 fold change [log 2 FC] ≤ −2 and ≥2 with a false discovery rate of FDR < 0.05). Additional information about the identified genes (e.g., FDR values, gene products, and pseudoCAP) are available in Supplementary Data 1