TABLE 2.

A. pleuropneumoniae genes which are upregulated during planktonic life over SJPL cellsa

Locus tagGeneDescriptionFold change
Hypothetical/unclassified/unknown
    APL_1839udpCOG2820: uridine phosphorylase, probable outer membrane protein, possible efflux protein3.937
    APL_1833COG2717: predicted membrane protein, conserved hypothetical protein3.388
    APL_1435Unassigned protein3.214
    APL_1285Hypothetical protein2.894
    APL_0145COG1611: predicted Rossmann fold nucleotide-binding protein2.726
    APL_1976yedFCOG0425: predicted redox protein, regulator of disulfide bond formation2.669
    APL_0116Hypothetical protein2.523
    APL_0093DUF1260 domain-containing protein2.020
    APL_1374Unassigned protein1.946
    APL_0465DUF74 domain-containing protein1.943
    APL_1919Predicted enzyme related to aldose 1 epimerase1.939
    APL_1138DUF526 domain-containing protein1.933
    APL_0443COG5295: autotransporter adhesin1.918
    APL_1656COG0561: predicted hydrolases of the HAD superfamily1.842
    APL_1203DUF479 domain-containing protein, hypothetical protein1.811
    APL_1609DUF533 domain-containing protein1.724
    APL_1881Putative carbamoylphosphate synthase large subunit1.703
    APL_1244Hypothetical protein1.555
Biosynthesis of cofactors
    APL_1622cbiMPredicted ABC cobalt transport permease protein CbiM2.419
    APL_0931iscSCysteine desulfurase, iron-sulfur cluster assembly2.374
    APL_0930nifUNifU-like protein, involved in Fe-S cluster formation2.011
    APL_1555hemLGlutamate-1-semialdehyde 2,1-aminomutase1.619
Energy metabolism
    APL_1832COG2041: sulfite oxidase and related enzymes13.073
    APL_0892fdxGFormate dehydrogenase, nitrate inducible, major subunit12.558
    APL_0895fdnIFormate dehydrogenase, cytochrome b556 subunit10.946
    APL_0894fdxHFormate dehydrogenase, iron-sulfur subunit6.0988
    APL_0687dldd-Lactate dehydrogenase5.442
    APL_0100nrfAAmmonia-forming cytochrome c552 nitrite reductase5.039
    APL_0106putABifunctional protein PutA4.634
    APL_0101nrfBNitrate reductase, cytochrome-c-type protein4.295
    APL_1091aspAAspartate ammonia lyase4.254
    APL_1528frdCFumarate reductase subunit C3.713
    APL_1137pgiGlucose-6-phosphate isomerase3.136
    APL_1959adhIAlcohol dehydrogenases 12.992
    APL_1414mqoPutative malate:quinone oxidoreductase2.802
    APL_1379ccpCytochrome c peroxidase2.796
    APL_1450fbpFructose-1,6-bisphosphatase2.528
    APL_1529frdAFumarate reductase, flavoprotein subunit2.420
    APL_0187pykAPyruvate kinase2.322
    APL_11973-Hydroxyacid dehydrogenase2.270
    APL_0102nrfCNitrate reductase2.250
    APL_1526frdDFumarate reductase subunit D2.178
    APL_0486maeAMalic enzyme (NADP dependent)2.074
    APL_1674dmsAAnaerobic dimethylsulfoxide reductase chain A precursor1.934
    APL_0483Predicted nitroreductase1.912
    APL_0084trxBThioredoxin reductase1.486
Transport and binding proteins: cations and iron
    APL_1265copACopper-transporting P-type ATPase1.518
Transport and binding proteins: others
    APL_0107putPNa+/proline symporter6.218
    APL_1173pnuCNicotinamide mononucleotide transporter2.448
    APL_0377glpTGlycerol-3-phosphate transporter2.331
    APL_1254COG0471: di- and tricarboxylate transporters2.237
    APL_1319ptsBPTS system sucrose-specific EIIBC component2.206
    APL_0447lctPl-Lactate permease2.204
    APL_0262modAMolybdate-binding periplasmic protein precursor2.049
    APL_1620cbiOPredicted ABC-type cobalt transport system, ATPase component1.902
    APL_1627Putative di- and tricarboxylate transporters1.876
    APL_1624cbiKPutative periplasmic binding protein CbiK1.823
    APL_1902yrhGCOG2116: formate/nitrite family of transporters1.718
    APL_1371ccmBHeme exporter protein B, cytochrome-c-type biogenesis protein1.596
Regulatory functions
    APL_108iclRPutative HTH-type transcriptional regulator2.832
    APL_0395rseAPutative sigma E factor negative regulatory protein2.260
    APL_0823glpRGlycerol-3-phosphate regulon repressor2.175
    APL_0997lacZBeta-galactosidase1.654
Transcription
    APL_1475rpoDRNA polymerase sigma 70 factor2.135
    APL_0560rhlBATP-dependent RNA helicase RhlB1.911
Purines, pyrimidines, nucleosides, and nucleotides
    APL_0646cpdB2′,3′-cyclic-nucleotide 2′-phosphodiesterase precursor2.087
Protein fate
    APL_0742degSProtease DegS precursor1.768
    APL_0871pepEPeptidase E1.686
Protein synthesis
    APL_0484rimKRibosomal protein S6 modification enzyme3.093
    APL_0146dusAtRNA-dihydrouridine synthase A2.456
Cellular processes
    APL_0004sodCCu/Zn superoxide dismutase precursor3.003
    APL_0251sodAManganese superoxide dismutase2.356
    APL_1241Probable carbon starvation protein A, predicted membrane protein2.098
    APL_1405oapACell envelope opacity-associated protein A1.793
Cell envelope
    APL_1494ftpADNA-binding ferritin-like protein (oxidative damage protectant), fine-tangled pilus major subunit (24-kDa surface protein)6.378
Fatty acid and phospholipid metabolism
    APL_0397lcfAAcyl-CoA synthetases (AMP forming)/AMP-acid ligases IIb1.746
Mobile and extrachromosomal element functions
    APL_1501Transposase2.078
    APL_0990Transposase1.814
    APL_0985Transposase1.680
DNA metabolism
    APL_1143recARecA recombinase1.491
Central intermediary metabolism
    APL_0109Possible 5-formyltetrahydrofolate cycloligase2.607
    APL_0375glpKGlycerol kinase2.316
  • a Eighty-two genes.

  • b CoA, coenzyme A.