TABLE 2.
Genes whose expression was strongly upregulated (>10-fold) in P. aeruginosa in the absence of sulfate relative to growth with inorganic sulfatea
| Gene name | Fold change in expression | % of S-amino acidsb | COGc | Protein description |
|---|---|---|---|---|
| PA0183 (atsA) | 32.95 | 1.87 | 3119 | Arylsulfatase |
| PA0184 (atsC) | 41.30 | 1.43 | 1116 | Probable ATP-binding component of ABC transporter |
| PA0185 (atsB) | 16.18 | 1.86 | 600 | Probable permease of ABC transporter |
| PA0186 (atsR) | 24.03 | 0.00 | 715 | Probable binding protein component of ABC transporter |
| PA0192 | 25.42 | 0.51 | 1629 | Probable TonB-dependent receptor |
| PA0193 (atsK) | 42.40 | 0.00 | 2175 | Alkylsulfatase |
| PA0194 | 26.92 | 0.00 | 2175 | Hypothetical protein |
| PA0197 (tonB2) | 38.60 | 0.74 | 810 | Hypothetical protein |
| PA0198 (exbB1) | 55.97 | 0.42 | 811 | Transport protein ExbB |
| PA0199 (exbD1) | 35.72 | 1.50 | 848 | Transport protein ExbD |
| PA2085 | 11.08 | 0.59 | 5517 | Probable ring-hydroxylating dioxygenase small subunit |
| PA2086 | 13.53 | 2.00 | 596 | Probable epoxide hydrolase |
| PA2087 | 12.16 | 2.75 | None | Hypothetical protein |
| PA2088 | 13.07 | 2.13 | 4106 | Hypothetical protein |
| PA2092 | 12.03 | 1.76 | 2814 | Probable MFS transporter |
| PA2292 | 13.41 | 4.30 | 3536 | Hypothetical protein |
| PA2293 | 20.70 | 1.25 | 1413 | Hypothetical protein |
| PA2294 | 22.32 | 3.87 | 1116 | Probable ATP-binding component of ABC transporter |
| PA2295 | 35.52 | 3.40 | 600 | Probable permease of ABC transporter |
| PA2296 | 44.80 | 0.85 | 715 | Hypothetical protein |
| PA2297 | 18.52 | 13.58 | 2221 | Probable ferredoxin |
| PA2298 | 14.83 | 4.70 | 1053 | Probable oxidoreductase |
| PA2299 | 19.46 | 2.41 | 2188 | Probable transcriptional regulator |
| PA2307 | 15.12 | 0.69 | 600 | Probable permease of ABC transporter |
| PA2308 | 15.43 | 2.13 | 1116 | Probable ATP-binding component of ABC transporter |
| PA2309 | 11.83 | 0.00 | 715 | Hypothetical protein |
| PA2310 | 10.81 | 1.02 | 2175 | Hypothetical protein |
| PA2324 | 26.10 | 0.48 | 1960 | Hypothetical protein |
| PA2325 | 14.64 | 0.00 | 1960 | Hypothetical protein |
| PA2326 | 11.14 | 1.07 | 2141 | Hypothetical protein |
| PA2346 | 24.30 | 0.73 | 1960 | Conserved hypothetical protein |
| PA2347 | 34.83 | 0.49 | 1960 | Hypothetical protein |
| PA2348 | 46.96 | 1.52 | 2141 | Conserved hypothetical protein |
| PA2349 | 36.85 | 0.00 | 1464 | Conserved hypothetical protein |
| PA2350 | 19.24 | 1.90 | 1135 | Probable ATP-binding component of ABC transporter |
| PA2351 | 10.54 | 4.61 | 2011 | Probable permease of ABC transporter |
| PA2354 | 16.04 | 1.06 | 3829 | Probable transcriptional regulator |
| PA2355 (msuC) | 22.58 | 1.78 | 1960 | Probable FMNH2-dependent monooxygenase |
| PA2356 (msuD) | 18.44 | 1.05 | 2141 | Methanesulfonate sulfonatase |
| PA2357 (msuE) | 17.80 | 0.00 | 431 | NADH-dependent FMN reductase |
| PA3447 | 13.47 | 2.41 | 1116 | Probable ATP-binding component of ABC transporter |
| PA3448 | 14.59 | 0.73 | 600 | Probable permease of ABC transporter |
| PA3954 | 20.21 | 0.27 | 2141 | Hypothetical protein |
Other sulfur sources were supplied for growth of P. aeruginosa. For a complete list of P. aeruginosa genes upregulated and downregulated (greater than twofold) under the conditions tested, see Table S3 in the supplemental material. Analysis was performed using Genespring GX 7.3, with a Benjamini-Hochberg multiple-testing correction and a false detection rate of 5%. Significance of the called genes was also assessed using SAM (49), giving q values of <0.05.
Percentages of sulfur-amino acids were calculated as the proportion of cysteine/methionine residues in the encoded protein, not including the initiating formylmethionine.
COG to which the gene has been assigned (46).