TABLE 1.

Effects of imipenem on genes of P. aeruginosa growing in biofilmsa

Gene no.bDescriptionFold change in expression level (P value)c
Day 1Day 2Day 3
0102Carbonic anhydrase5.9 (1.2E-2)2.5 (6.7E-3)1.4 (2.1E-1)
0320Hypothetical protein24.4 (7.2E-2)8.8 (6.1E-3)8.4 (9.6E-2)
0327Hypothetical protein5.3 (2.2E-2)3.3 (3.7E-2)2.3 (1.5E-1)
0376rpoH, sigma factor2.1 (2.9E-2)1.1 (3.1E-1)1.3 (1.5E-2)
0464creC, two-component sensor2.2 (1.3E-2)Δd1.0 (9.7E-1)
0465creD, inner membrane protein4.4 (1.0E-1)9.8 (1.2E-2)9.9 (9.8E-2)
0466Hypothetical protein5.0 (8.6E-2)7.0 (3.5E-2)8.7 (8.6E-2)
0755Probable porin1.2 (5.3E-1)6.6 (2.1E-3)5.5 (8.4E-2)
0762ealgU, sigma factor2.0 (1.6E-2)1.7 (1.1E-2)1.8 (4.4E-2)
0763mucA, anti-sigma factor2.0 (4.9E-3)1.7 (1.4E-3)1.8 (1.1E-1)
0764mucB, regulator, alginate biosynthesis2.2 (1.8E-2)1.5 (3.1E-1)1.3 (2.3E-1)
0765mucC, regulator, alginate biosynthesis2.4 (1.9E-3)1.1 (8.0E-1)1.2 (3.7E-1)
1071braF, amino acid transport protein−5.5 (1.0E-1)−1.1 (6.0E-1)1.5 (4.2E-2)
1078flgC, flagellar basal-body rod protein−5.0 (8.4E-3)−1.7 (1.8E-2)−2.3 (2.2E-1)
1079flgD, flagellar basal-body rod protein−3.9 (2.2E-2)−1.7 (7.8E-3)−2.6 (2.2E-1)
1080flgE, flagellar hook protein−4.1 (6.2E-4)−1.5 (1.8E-1)−2.4 (3.0E-1)
1081flgF, flagellar basal-body rod−2.8 (3.6E-2)−1.6 (3.1E-2)−2.6 (2.2E-1)
1084flgI, flagellar P-ring protein−2.2 (1.2E-2)−1.4 (1.6E-1)−2.2 (1.6E-1)
1178oprH, outer membrane protein H1 precursor6.1 (1.2E-3)5.0 (4.1E-4)3.2 (3.5E-2)
1179phoP, two-component regulator5.1 (1.3E-1)2.1 (1.1E-3)2.3 (1.5E-2)
1180phoQ, two-component sensor4.1 (4.6E-2)2.5 (1.0E-2)1.2 (4.4E-1)
1673Hypothetical protein−5.5 (2.0E-2)−1.3 (2.2E-1)1.0 (9.8E-1)
2247bkdA1, 2-oxoisovalerate dehydrogenase−5.5 (3.6E-2)−1.2 (3.3E-1)1.0 (8.6E-1)
2248bkdA2, 2-oxoisovalerate dehydrogenase−5.0 (1.8E-2)−1.1 (5.1E-1)1.0 (9.1E-1)
2367Hypothetical protein−5.3 (5.2E-4)−1.1 (7.8E-1)1.2 (6.4E-1)
2441Hypothetical protein1.5 (1.8E-1)2.4 (2.3E-2)5.6 (4.0E-3)
2513antB, anthranilate dioxygenase subunit−5.8 (1.8E-2)1.0 (9.8E-1)−1.2 (5.0E-1)
2658Hypothetical protein5.0 (1.7E-2)2.4 (1.5E-3)2.2 (8.0E-3)
2659Hypothetical protein7.2 (7.5E-3)3.4 (2.9E-4)3.3 (4.0E-2)
2760Probable outer membrane protein−5.0 (4.6E-2)−1.1 (5.6E-1)1.4 (3.0E-2)
3540algD, GDP-mannose 6-dehydrogenase11.1 (1.1E-1)10.5 (5.7E-3)3.6 (1.3E-1)
3541Alginate biosynthesis protein2.8 (2.2E-2)4.8 (2.4E-2)Δ
3542Alginate biosynthesis protein4.9 (8.6E-2)3.8 (2.5E-4)Δ
3543algK, alginate biosynthetic protein13.6 (2.0E-1)ΔΔ
3544algE, outer membrane protein3.3 (5.3E-2)3.7 (1.6E-3)Δ
3545algG, alginate-c5-mannuronan-epimerase4.1 (7.3E-2)6.0 (3.4E-4)Δ
3546algX, alginate biosynthesis protein4.2 (1.8E-2)3.3 (3.8E-3)Δ
3547algL, poly(beta-d-mannuronate) lyase5.6 (9.6E-2)3.0 (1.5E-3)1.3 (4.1E-1)
3548algI, alginate O-acetyltransferase2.8 (8.2E-2)2.8 (6.3E-3)Δ
3549algJ, alginate O-acetyltransferase6.5 (2.6E-2)2.8 (6.2E-4)Δ
3550algF, alginate O-acetyltransferase17.3 (4.1E-2)10.0 (3.8E-3)3.5 (2.1E-2)
3551algA, phosphomannose isomerase 5-diphospho-d-mannose pyrophosphorylase8.6 (5.0E-2)4.2 (3.6E-5)2.9 (9.9E-4)
3554Hypothetical protein5.1 (4.9E-2)1.5 (9.0E-2)1.4 (3.3E-1)
3559Probable nucleotide sugar dehydrogenase5.9 (1.7E-2)1.9 (3.8E-2)2.0 (1.1E-2)
3569mmsB, dehydrogenase−6.9 (9.6E-3)−1.7 (1.2E-2)−1.1 (5.0E-1)
3790oprC, outer membrane protein−5.3 (1.3E-2)−1.2 (6.7E-1)1.3 (1.9E-1)
4110ampC, β-lactamase precursor67.0 (9.5E-3)86.0 (5.5E-4)150.5 (3.3E-3)
4111Hypothetical protein18.8 (6.4E-4)13.0 (1.1E-3)14.8 (1.9E-2)
4112Probable sensor-response regulator2.3 (6.9E-3)1.2 (9.7E-2)1.4 (2.6E-1)
4306Hypothetical protein−6.5 (1.9E-2)−1.1 (7.9E-1)−1.1 (8.7E-1)
4407ftsZ, cell division protein1.3 (1.9E-1)2.5 (7.3E-3)2.7 (1.9E-4)
4408ftsA, cell division protein1.7 (3.4E-2)2.1 (8.1E-5)2.2 (2.3E-2)
4409ftsQ, cell division protein1.3 (1.6E-1)2.3 (1.2E-5)1.9 (9.3E-3)
4410ddlB, d-alanine-d-alanine ligase1.3 (3.0E-12.3 (7.0E-3)2.2 (4.5E-2)
4411murC, UDP-N-acetylmuramate-alanine ligase1.1 (2.3E-1)2.5 (3.5E-3)2.0 (1.6E-2)
4412murG, transferase1.5 (2.1E-1)2.4 (1.9E-3)2.6 (1.2E-2)
4413ftsW, cell division protein1.2 (2.6E-1)2.0 (3.9E-3)2.5 (4.8E-4)
4414murD, UDP-N-acetylmuramate-d-glutamate ligase1.1 (1.5E-1)2.1 (4.5E-4)2.4 (1.8E-3)
4415mraY, phospho-N-acetylmuramate-peptidyl transferase1.2 (2.9E-1)2.1 (1.3E-4)2.1 (3.1E-3)
4416murF, UDP-N-acetylmuramate-d-glutamyl- diaminopimelate-d-alanyl-d-alanyl ligase1.2 (5.8E-2)2.6 (2.3E-4)2.1 (4.1E-3)
4417murE, UDP-N-acetylmuramoylalanyl-d-glutamate- diaminopimelate ligase1.1 (3.2E-1)2.3 (2.7E-3)2.1 (7.7E-3)
4419ftsL, cell division protein1.0 (8.9E-1)2.4 (1.9E-3)2.6 (7.3E-3)
4420Hypothetical protein1.1 (5.2E-1)2.1 (1.6E-2)2.1 (4.7E-3)
4421Hypothetical protein−1.1 (3.6E-1)2.2 (9.9E-4)1.9 (8.4E-3)
4507Hypothetical protein−6.9 (1.7E-2)−2.1 (1.9E-2)−1.6 (1.1E-1)
4525pilA, type 4 fimbrial precursor−8.1 (3.5E-2)−1.8 (1.1E-1)−1.9 (2.9E-1)
4526pilB, type 4 fimbrial biogenesis protein−3.0 (2.7E-2)−1.3 (2.2E-1)−1.5 (1.8E-1)
5040pilQ, type 4 fimbrial biogenesis protein−2.5 (1.7E-2)−1.2 (3.3E-1)1.1 (5.9E-1)
5041pilP, type 4 fimbrial biogenesis protein−3.1 (1.6E-2)−1.1 (5.5E-1)−1.0 (8.7E-1)
5042pilO, type 4 fimbrial biogenesis protein−2.3 (6.0E-3)−1.2 (1.8E-1)1.1 (4.9E-1)
5044pilM, type 4 fimbrial biogenesis protein−2.1 (4.7E-2)−1.1 (4.9E-1)1.2 (4.1E-1)
5170arcD, arginine-ornithine antiporter−5.7 (2.3E-3)−1.4 (1.2E-1)−1.0 (9.4E-1)
5182Hypothetical protein6.0 (2.2E-2)3.5 (9.9E-4)2.7 (2.2E-3)
5261ealgR, alginate biosynthesis regulatory protein1.9 (1.2E-1)1.3 (1.9E-1)1.4 (2.0E-1)
5262ealgZ, alginate biosynthesis protein1.5 (2.8E-1)1.2 (4.3E-2)1.3 (2.0E-1)
5322ealgC, phosphomannomutase1.8 (1.3E-2)1.4 (4.6E-2)1.4 (2.9E-2)
  • a The table includes only a fraction (76 of 336) of the genes differentially expressed in response to imipenem. The complete list of all 336 differentially expressed genes is available at http://www.immi.ku.dk/bagge-arrays2003.

  • b Gene number from the P. aeruginosa genome project (http://www.pseudomonas.com). Genes indicated in boldface are mentioned in the text. Arrows indicate the transcriptional orientations of the operons of interest.

  • c E, × 10 (e.g., 1.2E−2 = 1.2 × 10−2).

  • d Δ, MAS 5.0 indicated that the signal was absent; i.e., the levels of expression were below the lower detection level of the chip.

  • e The gene was not significantly differentially expressed more than twofold on day 1, 2, or 3; but the trend for the gene may be of interest.