TABLE 2.
A. pleuropneumoniae genes which are upregulated during planktonic life over SJPL cellsa
| Locus tag | Gene | Description | Fold change |
|---|---|---|---|
| Hypothetical/unclassified/unknown | |||
| APL_1839 | udp | COG2820: uridine phosphorylase, probable outer membrane protein, possible efflux protein | 3.937 |
| APL_1833 | COG2717: predicted membrane protein, conserved hypothetical protein | 3.388 | |
| APL_1435 | Unassigned protein | 3.214 | |
| APL_1285 | Hypothetical protein | 2.894 | |
| APL_0145 | COG1611: predicted Rossmann fold nucleotide-binding protein | 2.726 | |
| APL_1976 | yedF | COG0425: predicted redox protein, regulator of disulfide bond formation | 2.669 |
| APL_0116 | Hypothetical protein | 2.523 | |
| APL_0093 | DUF1260 domain-containing protein | 2.020 | |
| APL_1374 | Unassigned protein | 1.946 | |
| APL_0465 | DUF74 domain-containing protein | 1.943 | |
| APL_1919 | Predicted enzyme related to aldose 1 epimerase | 1.939 | |
| APL_1138 | DUF526 domain-containing protein | 1.933 | |
| APL_0443 | COG5295: autotransporter adhesin | 1.918 | |
| APL_1656 | COG0561: predicted hydrolases of the HAD superfamily | 1.842 | |
| APL_1203 | DUF479 domain-containing protein, hypothetical protein | 1.811 | |
| APL_1609 | DUF533 domain-containing protein | 1.724 | |
| APL_1881 | Putative carbamoylphosphate synthase large subunit | 1.703 | |
| APL_1244 | Hypothetical protein | 1.555 | |
| Biosynthesis of cofactors | |||
| APL_1622 | cbiM | Predicted ABC cobalt transport permease protein CbiM | 2.419 |
| APL_0931 | iscS | Cysteine desulfurase, iron-sulfur cluster assembly | 2.374 |
| APL_0930 | nifU | NifU-like protein, involved in Fe-S cluster formation | 2.011 |
| APL_1555 | hemL | Glutamate-1-semialdehyde 2,1-aminomutase | 1.619 |
| Energy metabolism | |||
| APL_1832 | COG2041: sulfite oxidase and related enzymes | 13.073 | |
| APL_0892 | fdxG | Formate dehydrogenase, nitrate inducible, major subunit | 12.558 |
| APL_0895 | fdnI | Formate dehydrogenase, cytochrome b556 subunit | 10.946 |
| APL_0894 | fdxH | Formate dehydrogenase, iron-sulfur subunit | 6.0988 |
| APL_0687 | dld | d-Lactate dehydrogenase | 5.442 |
| APL_0100 | nrfA | Ammonia-forming cytochrome c552 nitrite reductase | 5.039 |
| APL_0106 | putA | Bifunctional protein PutA | 4.634 |
| APL_0101 | nrfB | Nitrate reductase, cytochrome-c-type protein | 4.295 |
| APL_1091 | aspA | Aspartate ammonia lyase | 4.254 |
| APL_1528 | frdC | Fumarate reductase subunit C | 3.713 |
| APL_1137 | pgi | Glucose-6-phosphate isomerase | 3.136 |
| APL_1959 | adhI | Alcohol dehydrogenases 1 | 2.992 |
| APL_1414 | mqo | Putative malate:quinone oxidoreductase | 2.802 |
| APL_1379 | ccp | Cytochrome c peroxidase | 2.796 |
| APL_1450 | fbp | Fructose-1,6-bisphosphatase | 2.528 |
| APL_1529 | frdA | Fumarate reductase, flavoprotein subunit | 2.420 |
| APL_0187 | pykA | Pyruvate kinase | 2.322 |
| APL_1197 | 3-Hydroxyacid dehydrogenase | 2.270 | |
| APL_0102 | nrfC | Nitrate reductase | 2.250 |
| APL_1526 | frdD | Fumarate reductase subunit D | 2.178 |
| APL_0486 | maeA | Malic enzyme (NADP dependent) | 2.074 |
| APL_1674 | dmsA | Anaerobic dimethylsulfoxide reductase chain A precursor | 1.934 |
| APL_0483 | Predicted nitroreductase | 1.912 | |
| APL_0084 | trxB | Thioredoxin reductase | 1.486 |
| Transport and binding proteins: cations and iron | |||
| APL_1265 | copA | Copper-transporting P-type ATPase | 1.518 |
| Transport and binding proteins: others | |||
| APL_0107 | putP | Na+/proline symporter | 6.218 |
| APL_1173 | pnuC | Nicotinamide mononucleotide transporter | 2.448 |
| APL_0377 | glpT | Glycerol-3-phosphate transporter | 2.331 |
| APL_1254 | COG0471: di- and tricarboxylate transporters | 2.237 | |
| APL_1319 | ptsB | PTS system sucrose-specific EIIBC component | 2.206 |
| APL_0447 | lctP | l-Lactate permease | 2.204 |
| APL_0262 | modA | Molybdate-binding periplasmic protein precursor | 2.049 |
| APL_1620 | cbiO | Predicted ABC-type cobalt transport system, ATPase component | 1.902 |
| APL_1627 | Putative di- and tricarboxylate transporters | 1.876 | |
| APL_1624 | cbiK | Putative periplasmic binding protein CbiK | 1.823 |
| APL_1902 | yrhG | COG2116: formate/nitrite family of transporters | 1.718 |
| APL_1371 | ccmB | Heme exporter protein B, cytochrome-c-type biogenesis protein | 1.596 |
| Regulatory functions | |||
| APL_108 | iclR | Putative HTH-type transcriptional regulator | 2.832 |
| APL_0395 | rseA | Putative sigma E factor negative regulatory protein | 2.260 |
| APL_0823 | glpR | Glycerol-3-phosphate regulon repressor | 2.175 |
| APL_0997 | lacZ | Beta-galactosidase | 1.654 |
| Transcription | |||
| APL_1475 | rpoD | RNA polymerase sigma 70 factor | 2.135 |
| APL_0560 | rhlB | ATP-dependent RNA helicase RhlB | 1.911 |
| Purines, pyrimidines, nucleosides, and nucleotides | |||
| APL_0646 | cpdB | 2′,3′-cyclic-nucleotide 2′-phosphodiesterase precursor | 2.087 |
| Protein fate | |||
| APL_0742 | degS | Protease DegS precursor | 1.768 |
| APL_0871 | pepE | Peptidase E | 1.686 |
| Protein synthesis | |||
| APL_0484 | rimK | Ribosomal protein S6 modification enzyme | 3.093 |
| APL_0146 | dusA | tRNA-dihydrouridine synthase A | 2.456 |
| Cellular processes | |||
| APL_0004 | sodC | Cu/Zn superoxide dismutase precursor | 3.003 |
| APL_0251 | sodA | Manganese superoxide dismutase | 2.356 |
| APL_1241 | Probable carbon starvation protein A, predicted membrane protein | 2.098 | |
| APL_1405 | oapA | Cell envelope opacity-associated protein A | 1.793 |
| Cell envelope | |||
| APL_1494 | ftpA | DNA-binding ferritin-like protein (oxidative damage protectant), fine-tangled pilus major subunit (24-kDa surface protein) | 6.378 |
| Fatty acid and phospholipid metabolism | |||
| APL_0397 | lcfA | Acyl-CoA synthetases (AMP forming)/AMP-acid ligases IIb | 1.746 |
| Mobile and extrachromosomal element functions | |||
| APL_1501 | Transposase | 2.078 | |
| APL_0990 | Transposase | 1.814 | |
| APL_0985 | Transposase | 1.680 | |
| DNA metabolism | |||
| APL_1143 | recA | RecA recombinase | 1.491 |
| Central intermediary metabolism | |||
| APL_0109 | Possible 5-formyltetrahydrofolate cycloligase | 2.607 | |
| APL_0375 | glpK | Glycerol kinase | 2.316 |
a
Eighty-two genes.
b
CoA, coenzyme A.