Table 1.
Functional classification of CDA-regulated genes obtained from DE gene list*.
| Gene family | Gene name or ID |
|---|---|
| Synthesis, sensing, and responding to CDA | PA4978-PA4980, PA4982-PA4983 |
| Flagellum and Type IV fimbrial biosynthesis, attachment, motility, and chemotaxis | fliCDFGJMNOQR, flhAB, fppA, fimX, tadCDGZ, flgBCDEGHI, motABC, fleQR, cheYZ, migA, ntrB, pilDEMOPRSUZ, pctAC, aer2, wspABCEFR, phoB, phoU, phoR, cupA3A4B2B5, PA0173-PA0178, PA1095, PA1103, PA1442, PA1458 -PA1459, PA1463-PA1464, PA1608, PA1930, PA2561, PA2573, PA2652, PA2654, PA2867, PA3348, PA4290, PA4300, PA4332, PA4457, PA4520, PA4633, PA4844, PA4915, PA5072 |
| Iron uptake | pvdADEFGJLNOPS, foxAR, fpvAR, prpL, toxR, rsaL, pfeR, pchCDFG, pprB, pcpS, PA0434-PA0435, PA0615, PA2402, PA2465, PA2468, PA4467, PA4471 |
| Fatty acid metabolism and transport | plsX, tktA, pgsA, gapA, glpD, lptA, hisB, ribB, faoA, pgk, gnyBH, accD, desB, fadD1, fabABDF1F2GH2IZ, uppS, mdcA, atuC,PA0098, PA0182,PA0286, PA0493, PA0506-PA0508, PA0745-PA0746, PA0879, PA1020-PA1022, PA1187, PA1240, PA1470, PA1535, PA1576, PA1628-PA1629, PA1631, PA1827, PA1869, PA2550, PA2552, PA2815, PA2841, PA2887-PA2891, PA2893, PA3286, PA3426, PA3589, PA3591, PA3593, PA3924,PA4089, PA4330, PA4912, PA4979-PA4980, PA4995, PA5020, PA5524 |
| Protein and Amino acid metabolism | thrS, folC, glnA, gmk, tgt, dadA, pauA3A5, gltX, gcvT1T2, glyQ, gdhA, valS, purD, trmD, speA, metGK, hutH, lysC, gpuA, mdlC, glnS, ansB, ileS, rpsBGILP, frr, groES, groEL, urea, lipB, sahH, betA, aspA, ilvCD, arc, aroC, proC, argC, nadBE, dapB, trpE, aotJ, phhA, phaF, PA0006, PA0400, PA0440, PA0530, PA1339-PA1342, PA1638, PA2084, PA2108, PA2740, PA3164, PA3271, PA3538, PA3589, PA3871, PA4180, PA4672, PA4774, PA4977, PA5093, PA5522 |
| Amino acid and Fatty acid metabolism | gcdH |
| Carbohydrate transport and metabolism | rpe, eno, ppsA, tpiA, pykF, pgm, chiC, PA3430 |
| Nucleotide transport and metabolism | cyaA, ndk, guaA, xpt, xdhA, purHLMN, pyrDEFH Q, nrdD,cmk, PA0148, PA0387, PA0439, PA3004, PA3516-PA3517,PA4645 |
| Amino acid and Nucleotide metabolism | carAB, prs, purBF, pyrB, PA4758 |
| Coenzyme transport and metabolism | cobABLV, folE1E2X, pdxJ, moaA1A2C, thiDl |
| Transcription regulators | rpoD, rpoN, PA0436, PA0512-PA0513, PA0515, PA1201,PA1399, PA1630, PA1859, PA2273, PA2432, PA2885, PA5403 |
| EPS and LPS synthesis and secretion | algABCDEFGIJLQRUWXZ, alg8, alg44, kdsA, pelABD, ddlA, pslB, mucBCD, wzt, waaACFG, rfaDE, wbpMWZ, wapR, lpxDO2, rmd, rmlC, PA1390, PA3242, PA3256, PA5238, PA5291 |
| Aerobic and Anaerobic respiration | azuA, narHIJK1, nasA, nirBCDFJLMNQS, ackA, nosDRZ, rubB napCF, nuoD, aer, ubiA, ercS, norD, etfB, hemE, PA0510, PA0516, PA0918, PA1779, PA3025, PA3491, PA4772, PA5491 |
| Bacteriophage production | PA0616-PA0623, PA0627, PA063 |
| Tricarboxylic acid (TCA) cycle | fumC1, acnA |
| N-AHLs and PQS QS-dependent genes and Virulence | lasIR, rhlI, qscR, rsaL, vfr, pqsR (mvfR), pchR, gacA,pqsBCDEH, antAB, rpoS, xcpTVW, secA, pscT, pcrD, aprA,toxA, katAB, sodBM, lasB, phzD1D2M, phoA, Hxc VUW,PA0682, PA0628, PA0684-PA0685, PA0687, PA4304 |
| Signal transduction mechanisms | irlR, pprAB, mifS, bfiRS, PA0431, PA0756, PA0847, PA0930,PA1107, PA1335-PA1336, PA1437-PA1438, PA1782, PA2479-PA2480, PA2524, PA2572, PA2656, PA2766, PA2824, PA3077- PA3078, PA3376, PA3946, PA4197, PA4332, PA4886, PA5487 |
| Protection and Adaptation | pcoB, csaA, sspB, surE, trxA, tpx, ahpCF, recA, hslV, grpE, copRS, czcR, phoP, pmrAB, parR, betC, envZ-ompR, lon, asrA, PA0456, PA0961, PA0706, PA2092, PA2521, PA2701, PA2812, PA4218, PA4222-PA4223, PA4775, PA5159, PA5471 |
| Membrane component and transporters | pstAB, opdH, exbB1, fiuA, PA0581, PA0751-PA0752, PA0754, PA2042, PA2350, PA2658-PA2659, PA3212, PA3376, PA3671 |
| Replication, recombination and repair | gyrA, mutL, uvrA, hepA, recG, mica, ruvB, asp |
| Transcription | rpoACNZ, rhlB, PA2840 |
| Translation | infBC, tsf, truB, pnp, miaA, rnd, PA0733, PA1678, PA4673 |
| Post-translational modification | dnaJK, clpB, clpXP, clpP2, tig, gcp, dsbG, msrA, PA0473,PA2478, PA3450 |
| Cell cycle | ftsHZY, gidA, mreB, cafA, mind |
| Hypothetical proteins | PA0089, PA0193, PA0333, PA0338, PA0429, PA0433, PA0581, PA0754, PA0841, PA0935, PA0939, PA0979, PA0982, PA1016, PA1096, PA1149, PA1167, PA1367, PA1571, PA1814, PA1925, PA2137, PA2189, PA2412, PA2464, PA2506, PA2651, PA2659, PA2689, PA2771, PA2780, PA2829, PA2842, PA2958, PA2971, PA3070, PA3143, PA3216, PA3219, PA3229, PA3273, PA3402, PA3762, PA3772, PA3793, PA3869, PA3962, PA4149, PA4202, PA4298-PA4299, PA4395, PA4399, PA4404-PA4405, PA4510, PA4562,PA4884, PA4962, PA5237, PA5463, PA5492, PA5536 |
*
The detailed information is provided in Tables S2, S3.