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Table II.
A. pleuropneumoniae strain S4074 genes that are up- or down-regulated after growth in BHI-B compared to growth in BHI-A.
| Locus tag | Gene | Description | Fold change |
|---|---|---|---|
| Amino acid biosynthesis | |||
| APL_0728 | ilvH | Acetolactate synthase small subunit | 5.707 |
| APL_0662 | aspC | Putative aspartate aminotransferase | 5.324 |
| APL_0427 | gdhA | NADP-specific glutamate dehydrogenase | 4.943 |
| APL_0727 | ilvI | Acetolactate synthase large subunit | 4.204 |
| APL_0099 | ilvG | Acetolactate synthase isozyme II large subunit (AHAS-II) | 3.915 |
| APL_1499 | thrC | Threonine synthase | 3.198 |
| APL_0097 | ilvD | Dihydroxy-acid dehydratase | 3.142 |
| APL_0393 | leuA | 2-isopropylmalate synthase | 3.000 |
| APL_0098 | ilvM | Acetolactate synthase isozyme II small subunit (AHAS-II) | 2.934 |
| APL_2027 | hisF | Imidazole glycerol phosphate synthase subunit hisF | 2.833 |
| APL_0702 | serC | Phosphoserine aminotransferase | 2.788 |
| APL_0432 | leuB | 3-isopropylmalate dehydrogenase | 2.643 |
| APL_0899 | dapA | Dihydrodipicolinate synthase | 2.401 |
| APL_0211 | glyA | Glycine/serine hydroxymethyltransferase | 2.398 |
| APL_0133 | cysB | HTH-type transcriptional regulator CysB | 2.340 |
| APL_1853 | ilvC | Ketol-acid reductoisomerase | 2.313 |
| APL_0072 | ilvE | Branched-chain-amino-acid aminotransferase | 2.001 |
| APL_0859 | trpCF | Tryptophan biosynthesis protein trpCF | 1.883 |
| APL_2025 | hisH | Imidazole glycerol phosphate synthase subunit hisH | 1.777 |
| APL_2026 | hisA | Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase | 1.739 |
| APL_1198 | APL_1198 | Putative NAD(P)H nitroreductase | 1.708 |
| APL_0139 | leuC | 3-isopropylmalate dehydratase large subunit 2 | 1.605 |
| APL_1230 | serB | Phosphoserine phosphatase | 1.438 |
| APL_0620 | aroG | Phospho-2-dehydro-3-deoxyheptonate aldolase | 1.428 |
| APL_1873 | dapE | Succinyl-diaminopimelate desuccinylase | 1.380 |
| Biosynthesis of cofactors, prosthetic groups, and carriers | |||
| APL_0207 | Dxs | 1-deoxy-D-xylulose-5-phosphate synthase (DXPS) | −1.555 |
| APL_1461 | menA | 1,4-dihydroxy-2-naphthoateoctaprenyltransferase | −1.631 |
| APL_0382 | ribD | Riboflavin biosynthesis protein | −1.726 |
| APL_1408 | gshA | Glutathione biosynthesis bifunctional protein GshAB | −1.789 |
| Cell envelope | |||
| APL_1494 | ftpA | Fine tangled pili major subunit | 5.705 |
| APL_1921 | pgaA | Biofilm PGA synthesis protein PgaA precursor | 5.308 |
| APL_0460 | plpD | Lipoprotein Plp4 | 3.801 |
| APL_1923 | pgaC | Biofilm PGA synthesis N-glycosyltransferase PgaC | 3.591 |
| APL_1922 | pgaB | Biofilm PGA synthesis lipoprotein PgaB precursor | 3.093 |
| APL_0006 | ompP2A | Outer membrane protein P2 | 2.515 |
| APL_0550 | tadC | Tight adherence protein C | 1.985 |
| APL_0442 | sanA | SanA protein | 1.776 |
| APL_0549 | tadD | Tight adherence protein D | 1.749 |
| APL_0332 | hlpB | Lipoprotein HlpB | 1.627 |
| APL_1364 | gmhA | Putative phosphoheptose isomerase | 1.386 |
| APL_0873 | rlpB | Putative rare lipoprotein B | −1.391 |
| APL_1028 | APL_1028 | Possible lipooligosaccharide N-acetylglucosamine glycosyltransferase | −1.445 |
| APL_0747 | mepA | Penicillin-insensitive murein endopeptidase precursor | −1.446 |
| APL_0436 | mreC | Rod shape-determining protein MreC | −1.585 |
| APL_1086 | ompW | Outer membrane protein W precursor | −1.606 |
| APL_1029 | APL_1029 | Hypothetical protein | −1.650 |
| APL_1424 | oxaA | Inner membrane protein OxaA | −1.772 |
| APL_0933 | ompP1 | Putative outer membrane protein precursor | −2.808 |
| Cellular processes | |||
| APL_1489 | Tpx | Putative thiol peroxidase | 2.252 |
| APL_0988 | hktE | Catalase | −1.461 |
| APL_0669 | APL_0669 | Putative iron dependent peroxidase | −1.483 |
| APL_1442 | apxID | RTX-I toxin secretion component | −1.506 |
| APL_1346 | ftsY | Cell division protein FtsY-like protein | −1.530 |
| Central intermediary metabolism | |||
| APL_1615 | Gst | Putative glutathione S-transferase | 3.269 |
| APL_1614 | ureE | Urease accessory protein UreE | 2.601 |
| APL_1613 | ureF | Urease accessory protein UreF | 2.478 |
| APL_1612 | ureG | Urease accessory protein UreG | 2.165 |
| APL_1618 | ureA | Urease gamma subunit UreA | 1.653 |
| DNA metabolism | |||
| APL_1931 | tagI | 3-methyladenine-DNA glycosidase | −1.500 |
| APL_1474 | dnaG | DNA primase | −1.551 |
| APL_1282 | dnaQ | DNA polymerase III subunit | −1.579 |
| APL_1255 | parE | DNA topoisomerase IV subunit | −1.630 |
| APL_1505 | holC | DNA polymerase III subunit | −1.663 |
| Energy metabolism | |||
| APL_1197 | APL_1197 | 3-hydroxyacid dehydrogenase | 3.100 |
| APL_0841 | pntB | NAD(P) transhydrogenase subunit beta | 2.726 |
| APL_1908 | xylA | Xylose isomerase | 2.243 |
| APL_0894 | fdxH | Formate dehydrogenase, iron-sulfur subunit | 2.161 |
| APL_1425 | napC | Cytochrome c-type protein NapC | 2.159 |
| APL_1799 | torC | Pentahemic c-type cytochrome | 2.156 |
| APL_0892 | fdxG | Formate dehydrogenase, nitrate-inducible, major subunit | 2.116 |
| APL_1798 | torA | Trimethylamine-N-oxide reductase precursor | 1.977 |
| APL_0381 | glpC | Anaerobic glycerol-3-phosphate dehydrogenase subunit C | 1.919 |
| APL_0842 | pntA | NAD(P) transhydrogenase subunit alpha | 1.903 |
| APL_0895 | fdnI | Formate dehydrogenase, cytochrome b556 subunit | 1.816 |
| APL_1208 | adhC | Putative alcohol dehydrogenase class 3 | 1.801 |
| APL_0971 | APL_0971 | Putative acyl CoA thioester hydrolase | 1.796 |
| APL_0652 | manB | Phosphomannomutase | 1.677 |
| APL_0483 | APL_0483 | Predicted nitroreductase | 1.668 |
| APL_0142 | glxK | Glycerate kinase | 1.564 |
| APL_0452 | sucC | Succinyl-CoA synthetase beta chain | 1.515 |
| APL_0461 | APL_0461 | Predicted hydrolases of the HAD superfamily | 1.456 |
| APL_0687 | Dld | D-lactate dehydrogenase | 1.439 |
| APL_1510 | gpsA | Glycerol-3-phosphate dehydrogenase (NAD(P)+) | 1.414 |
| APL_1427 | napH | Ferredoxin-type protein NapH-like protein | 1.360 |
| APL_0789 | APL_0789 | Dioxygenase | 1.253 |
| APL_0983 | tktA | Transketolase 2 | 1.233 |
| APL_1036 | pflB | Formate acetyltransferase | −1.653 |
| APL_1498 | mgsA | Methylglyoxal synthase | −1.790 |
| APL_1840 | ubiC | 4-hydroxybenzoate synthetase (chorismate lyase) | −1.952 |
| APL_0857 | sdaA | L-serine dehydratase | −3.016 |
| Fatty acid and phospholipid metabolism | |||
| APL_1407 | Psd | Phosphatidylserine decarboxylase | −1.419 |
| APL_1384 | fabH | 3-oxoacyl-[acyl-carrier-protein] synthase 3 | −1.826 |
| APL_1385 | plsX | Fatty acid/phospholipid synthesis protein PlsX | −2.706 |
| Mobile and extrachromosomal element functions | |||
| APL_1056 | APL_1056 | Transposase | 1.560 |
| APL_0985 | APL_0985 | Transposase | 1.271 |
| Protein fate | |||
| APL_0871 | pepE | Peptidase E | 2.551 |
| APL_1101 | pepA | Putative cytosol aminopeptidase | 1.913 |
| APL_0254 | pepD | Aminoacyl-histidine dipeptidase | 1.903 |
| APL_1883 | ptrA | Protease 3 precursor | 1.680 |
| APL_0928 | hscB | Co-chaperone protein HscB-like protein | 1.377 |
| APL_1068 | secF | Protein-export membrane protein SecF | −1.496 |
| APL_0321 | dsbB | Disulfide bond formation protein B | −1.557 |
| APL_1035 | pflA | Pyruvate formate-lyase 1-activating enzyme | −1.774 |
| Protein synthesis | |||
| APL_1821 | rpmE | 50S ribosomal protein L31 | 2.211 |
| APL_0484 | rimK | Ribosomal protein S6 modification protein | 1.533 |
| APL_1781 | rpsM | 30S ribosomal protein S13 | −1.401 |
| APL_0205 | APL_0205 | Predicted rRNA methyltransferase | −1.538 |
| APL_0399 | ksgA | Dimethyladenosine transferase | −1.578 |
| APL_0679 | glnS | Glutaminyl-tRNA synthetase | −1.584 |
| APL_0641 | truB | tRNA pseudouridine synthase B | −1.742 |
| APL_1383 | trmB | tRNA (guanine-N(7)-)-methyltransferase | −1.756 |
| APL_0574 | APL_0574 | tRNA-specific adenosine deaminase | −1.778 |
| APL_0723 | Tgt | Queuine tRNA-ribosyltransferase | −1.937 |
| Purines, pyrimidines, nucleosides, and nucleotides | |||
| APL_0958 | purH | Bifunctional purine biosynthesis protein PurH | 1.856 |
| APL_0593 | guaB | Inosine-5′-monophosphate dehydrogenase | 1.485 |
| APL_1343 | Cdd | Cytidine deaminase | 1.278 |
| APL_1014 | deoD | Purine nucleoside phosphorylase DeoD-like protein | −1.430 |
| APL_0351 | Ndk | Nucleoside diphosphate kinase | −1.531 |
| APL_1839 | Udp | Uridine phosphorylase | −1.617 |
| APL_1075 | purA | Adenylosuccinate synthetase | −1.762 |
| Regulatory functions | |||
| APL_0059 | narP | Nitrate/nitrite response regulator protein | 2.552 |
| APL_0823 | glpR | Glycerol-3-phosphate regulon repressor | 1.908 |
| APL_1295 | argR | Arginine repressor | 1.896 |
| APL_0126 | APL_0126 | HIT-like protein | 1.580 |
| APL_0395 | rseA | Putative sigma-E factor negative regulatory protein | 1.524 |
| APL_1668 | rbsR | Ribose operon repressor | 1.302 |
| APL_1270 | sprT | Putative SprT-like protein | −1.483 |
| APL_1233 | malT | HTH-type transcriptional regulator MalT | −1.484 |
| APL_1540 | tldD | TldD-like protein | −1.578 |
| Transcription | |||
| APL_0560 | rhlB | ATP-dependent RNA helicase RhlB | 1.409 |
| APL_0423 | rnhA | Ribonuclease HI | 1.345 |
| APL_0201 | nusB | Transcription antitermination protein NusB | −1.457 |
| Transport and binding proteins | |||
| APL_0967 | gltS | Sodium/glutamate symport carrier protein | 4.155 |
| APL_0377 | glpT | Glycerol-3-phosphate transporter | 3.247 |
| APL_0064 | dppA | Periplasmic dipeptide transport protein | 3.168 |
| APL_0869 | abgB | Aminobenzoyl-glutamate utilization-like protein | 3.004 |
| APL_1857 | merP | Copper chaperone MerP | 2.911 |
| APL_0068 | dppF | Dipeptide transport ATP-binding protein DppF | 2.860 |
| APL_1665 | gntP_1 | Gluconate permease | 2.723 |
| APL_0066 | dppC | Dipeptide transport system permease protein DppC | 2.640 |
| APL_1440 | znuA | High-affinity zinc uptake system protein ZnuA precursor | 2.600 |
| APL_0065 | dppB | Dipeptide transport system permease protein DppB | 2.229 |
| APL_0067 | dppD | Dipeptide transport ATP-binding protein DppD | 2.036 |
| APL_1448 | afuC | Ferric ABC transporter ATP-binding protein | 1.855 |
| APL_1319 | ptsB | PTS system sucrose-specific EIIBC component | 1.744 |
| APL_1320 | thiQ | Thiamine transport ATP-binding protein ThiQ | 1.569 |
| APL_1622 | cbiM | Predicted ABC transport permease protein CbiM | 1.433 |
| APL_1620 | cbiO | Predicted ABC transport ATP-binding protein CbiO | 1.417 |
| APL_1173 | pnuC | Nicotinamide mononucleotide transporter | 1.408 |
| APL_0749 | APL_0749 | Potassium efflux system KefA | −1.436 |
| APL_1212 | tehA | Tellurite resistance protein TehA | −1.543 |
| APL_0716 | APL_0716 | Iron(III) ABC transporter, permease protein | −1.547 |
| APL_1253 | APL_1253 | Putative sodium/sulphate transporter | −1.598 |
| APL_1846 | cysT | Sulfate transport system permease protein cysT | −1.684 |
| APL_0191 | APL_0191 | Predicted Na+-dependent transporter of the SNF family | −1.751 |
| APL_1083 | arcD | Putative arginine/ornithine antiporter | −1.786 |
| APL_2016 | fhuA | Ferrichrome-iron receptor FhuA | −2.031 |
| APL_1847 | cysW | Sulfate transport system permease protein cysW | −2.195 |
| APL_1844 | cysN | Sulphate adenylate transferase subunit 1 | −2.375 |
| APL_1848 | cysA | Sulfate/thiosulfate import ATP-binding protein cysA | −2.401 |
| APL_1843 | cysJ | Sulfite reductase [NADPH] flavoprotein alpha-component | −2.757 |
| APL_1127 | APL_1127 | Predicted Na+/alanine symporter | −3.402 |
| Hypothetical/unknown/unclassified | |||
| APL_1100 | APL_1100 | Hypothetical protein | 3.395 |
| APL_0920 | APL_0920 | Hypothetical protein | 2.835 |
| APL_1882 | APL_1882 | Hypothetical protein | 2.776 |
| APL_1856 | APL_1856 | Hypothetical protein | 2.775 |
| APL_1855 | APL_1855 | Hypothetical protein | 2.763 |
| APL_0443 | APL_0443 | Autotransporter adhesin | 2.762 |
| APL_1252 | APL_1252 | Hypothetical protein | 2.739 |
| APL_0134 | APL_0134 | Hypothetical protein | 2.681 |
| APL_0836 | APL_0836 | Putative transcriptional regulator | 2.661 |
| APL_1588 | APL_1588 | Predicted TRAP transporter solute receptor | 2.464 |
| APL_1491 | APL_1491 | Hypothetical protein | 2.282 |
| APL_0104 | APL_0104 | Autotransporter adhesin | 2.231 |
| APL_1069 | ftnA | Ferritin-like protein 1 | 2.194 |
| APL_1059 | APL_1059 | Hypothetical transposase-like protein | 2.172 |
| APL_1690 | APL_1690 | Inner membrane protein | 2.168 |
| APL_0245 | APL_0245 | Transferrin binding protein-like solute binding protein | 2.097 |
| APL_1191 | namA | NADPH dehydrogenase | 2.078 |
| APL_1948 | APL_1948 | Hypothetical protein | 2.061 |
| APL_0870 | APL_0870 | Putative C4-dicarboxylate transporter | 2.034 |
| APL_0643 | APL_0643 | Hypothetical protein | 2.029 |
| APL_1743 | APL_1743 | Ser/Thr protein phosphatase family protein | 1.999 |
| APL_0426 | APL_0426 | Hypothetical protein | 1.994 |
| APL_1791 | APL_1791 | Putative periplasmic iron/siderophore binding protein | 1.944 |
| APL_0970 | APL_0970 | Hypothetical protein | 1.908 |
| APL_1070 | ftnB | Ferritin-like protein 2 | 1.907 |
| APL_1894 | APL_1894 | Hypothetical protein | 1.907 |
| APL_1374 | APL_1374 | Hypothetical protein | 1.803 |
| APL_1206 | APL_1206 | Plasmid stability-like protein | 1.794 |
| APL_1881 | APL_1881 | Hypothetical protein | 1.792 |
| APL_0038 | APL_0038 | Hypothetical protein | 1.730 |
| APL_1355 | APL_1355 | Hypothetical protein | 1.716 |
| APL_0471 | APL_0471 | Hypothetical protein | 1.707 |
| APL_1438 | APL_1438 | Hypothetical protein | 1.689 |
| APL_1437 | APL_1437 | Hypothetical protein | 1.643 |
| APL_1423 | APL_1423 | Hypothetical protein | 1.612 |
| APL_0125 | APL_0125 | Hypothetical protein | 1.608 |
| APL_0096 | APL_0096 | Zinc transporter family protein ZIP | 1.592 |
| APL_0220 | APL_0220 | Putative lipoprotein | 1.583 |
| APL_1934 | APL_1934 | Hypothetical protein | 1.570 |
| APL_1574 | APL_1574 | Hypothetical protein | 1.543 |
| APL_0036 | APL_0036 | Hypothetical protein | 1.533 |
| APL_0222 | APL_0222 | Putative lipoprotein | 1.518 |
| APL_1088 | APL_1088 | Hypothetical protein | 1.512 |
| APL_1207 | APL_1207 | Hypothetical protein | 1.510 |
| APL_0463 | APL_0463 | Predicted sortase and related acyltransferases | 1.448 |
| APL_1859 | APL_1859 | Probable NADH-dependent butanol dehydrogenase 1 | 1.448 |
| APL_1828 | APL_1828 | PilT protein-like protein | 1.447 |
| APL_0433 | msrB | Methionine sulfoxide reductase B | 1.415 |
| APL_1189 | APL_1189 | Hypothetical protein | 1.393 |
| APL_0090 | APL_0090 | Hypothetical protein | 1.360 |
| APL_1709 | APL_1709 | Hypothetical protein | −1.307 |
| APL_0357 | APL_0357 | Hypothetical protein | −1.328 |
| APL_1380 | APL_1380 | Hypothetical protein | −1.394 |
| APL_1729 | APL_1729 | Hypothetical protein | −1.401 |
| APL_1062 | APL_1062 | Hypothetical protein | −1.468 |
| APL_0179 | APL_0179 | Hypothetical protein | −1.481 |
| APL_0940 | APL_0940 | Hypothetical protein | −1.482 |
| APL_1273 | APL_1273 | Putative fimbrial biogenesis and twitching motility protein PilF-like protein | −1.488 |
| APL_1131 | APL_1131 | Hypothetical protein | −1.540 |
| APL_0583 | APL_0583 | Hypothetical protein | −1.585 |
| APL_1096 | APL_1096 | Hypothetical protein (59% ID dispersine B) | −1.594 |
| APL_0936 | APL_0936 | Hypothetical protein | −1.616 |
| APL_1115 | APL_1115 | Hypothetical protein | −1.639 |
| APL_0811 | APL_0811 | Hypothetical protein | −1.682 |
| APL_1898 | ap2029 | Hypothetical protein | −1.798 |
| APL_1654 | gidB | Methyltransferase GidB | −1.816 |
| APL_0340 | APL_0340 | Hypothetical protein | −1.893 |
| APL_1381 | APL_1381 | Hypothetical protein | −1.926 |
| APL_0053 | typA | GTP-binding protein | −2.043 |
| APL_1681 | APL_1681 | Hypothetical protein | −2.233 |