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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
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
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