Table 1.
Transcriptional characteristics of the genes within the nitrogen fixation island of P. stutzeri A1501
| Gene name | Functional description | Ammonium shocka | Nitrogen fixationb | Consensus sequencec | ||
|---|---|---|---|---|---|---|
| NifA | RpoN | |||||
| PST1302 | glutaredoxin-related protein | 0.06 | 16.83 | |||
| PST1303 | thiosulfate sulfurtransferase glpE | 0.03 | 53.99 | |||
| PST1304 | nifQ | nitrogen fixation protein NifQ | 0.03 | 46.56 | ||
| PST1305 | arsenate reductase related protein | 0.03 | 38.67 | |||
| PST1306 | nifB | FeMo cofactor biosynthesis protein NifB | 0.06 | 21.46 | Yes | Yes |
| PST1307 | conserved hypothetical protein | 0.57 | 1.87 | No | Yes | |
| PST1308 | transcriptional regulator, LysR family | 0.43 | 2.22 | No | No | |
| PST1309 | conserved hypothetical protein | 0.84 | 1.12 | No | No | |
| PST1310 | transcriptional regulator, AraC family | 1.03 | 1.02 | No | No | |
| PST1311 | fosmidomycin resistance protein | 0.81 | 1.34 | No | Yes | |
| PST1312 | tpmA | thiopurine s-methyltransferase | 0.34 | 2.65 | No | Yes |
| PST1313 | nifA | positive regulatory protein | 0.15 | 6.95 | ||
| PST1314 | nifL | negative regulatory protein | 0.12 | 7.68 | Yes | Yes |
| PST1315 | rnfA | electron transport complex, A subunit | 0.37 | 2.66 | Yes | Yes |
| PST1316 | rnfB | electron transport complex, B subunit | 0.10 | 9.94 | ||
| PST1317 | rnfC | electron transport complex, C subunit | 0.49 | 2.22 | ||
| PST1318 | rnfD | electron transport complex, D subunit | 0.13 | 7.67 | ||
| PST1319 | rnfG | electron transport complex, G subunit | 0.16 | 7.47 | ||
| PST1320 | rnfE | electron transport complex, E subunit | 0.15 | 8.80 | ||
| PST1321 | rnfH | electron transport complex, H subunit | 0.21 | 17.55 | ||
| PST1322 | nifY2 | iron-molybdenum cofactor biosynthesis protein | 0.10 | 21.74 | ||
| PST1323 | nitrogen fixation-related protein | 0.18 | 13.73 | |||
| PST1324 | conserved hypothetical protein | 0.15 | 25.99 | |||
| PST1325# | conserved hypothetical protein | 0.15 | 9.68 | Yes | Yes | |
| PST1326 | nifH | Fe protein | 0.32 | 94.05 | Yes | Yes |
| PST1327 | nifD | MoFe protein, alpha subunit | 0.56 | 54.16 | ||
| PST1328 | nifK | MoFe protein, beta subunit | 0.62 | 38.22 | ||
| PST1329 | nifT | nitrogen fixation protein | 1.70 | 7.82 | ||
| PST1330 | nifY | iron-molybdenum cofactor biosynthesis protein | 0.33 | 8.51 | ||
| PST1331 | conserved hypothetical protein | 0.41 | 12.55 | |||
| PST1332 | leucine-rich repeat domain protein | 0.57 | 3.27 | No | Yes | |
| PST1333 | nifE | iron-molybdenum cofactor biosynthesis protein | 0.05 | 35.82 | Yes | Yes |
| PST1334 | nifN | iron-molybdenum cofactor biosynthesis protein | 0.07 | 13.32 | ||
| PST1335 | nifX | iron-molybdenum cofactor biosynthesis protein | 0.10 | 37.97 | ||
| PST1336 | protein of unknown function DUF269 | 0.29 | 5.06 | |||
| PST1337 | protein of unknown function DUF683 | 0.05 | 63.84 | |||
| PST1338 | ferredoxin, 4Fe-4S | 0.08 | 31.07 | Yes | Yes | |
| PST1339 | ferredoxin, 2Fe-2S | 0.76 | 2.94 | |||
| PST1340 | conserved hypothetical protein | 0.82 | 1.28 | |||
| PST1341 | conserved hypothetical protein | 0.85 | 1.28 | |||
| PST1342 | conserved hypothetical protein | 0.43 | 3.69 | |||
| PST1343 | conserved hypothetical protein | 0.70 | 2.56 | |||
| PST1344 | conserved hypothetical protein | 0.21 | 7.16 | Yes | Yes | |
| PST1345 | modC | molybdenum transport protein ModC | 0.79 | 1.59 | ||
| PST1346 | modB | molybdate ABC transporter | 0.48 | 2.05 | ||
| PST1347 | modA | molybdenum ABC transporter | 0.20 | 4.12 | ||
| PST1348 | putative molybdenum-binding protein | 0.22 | 3.88 | Yes | Yes | |
| PST1349 | hesB | Fe-S cluster assembly protein | 0.07 | 20.92 | Yes | Yes |
| PST1350 | nifU | Fe-S cluster assembly protein NifU | 0.11 | 10.77 | ||
| PST1351 | nifS | nitrogenase metalloclusters biosynthesis protein | 0.11 | 16.21 | ||
| PST1352 | nifV | homocitrate synthase | 0.05 | 24.55 | ||
| PST1353 | cysE | serine acetyltransferase (cysE-like) | 0.05 | 32.98 | ||
| PST1354 | conserved hypothetical protein | 0.10 | 11.11 | |||
| PST1355 | nifW | nitrogenase stabilizing/protective protein | 0.16 | 26.04 | ||
| PST1356 | nifZ | Fe-S cofactor synthesis protein | 0.17 | 18.17 | ||
| PST1357 | nifM | putative peptidyl-prolyl cis/trans isomerase | 0.19 | 18.78 | ||
| PST1358 | ATP-dependent Clp protease | 0.56 | 8.42 | |||
| PST1359 | nifF | flavodoxin for electron transfer | 0.86 | 14.91 | Yes | Yes |
aInduction ratio (ammonium shock conditions/nitrogen fixation conditions) after exposure of bacteria to 20 mM ammonia for 10 min.
bInduction ratio (nitrogen fixation conditions/nitrogen-excess conditions).
cORF(s) preceded by a consensus sequence that resembles the NifA or RpoN consensus sequence for A1501. The predicted NifA-σ54-dependent operons are shown in Figure 2B.
#Also designated pnfA in this study.