TABLE 2.

Expression ratio values of the genes showing largest regulatory responses to growth in mixed culturea

Category and locus tagGeneCOG nameExpression ratio (mixed culture/monoculture)
3.5 h5.5 h8 h12 h
Folic acid metabolism
    LBUL_0208Dihydroneopterin aldolase0.880.431.282.25
    LBUL_0209GTP cyclohydrolase I0.400.321.351.64
    LBUL_0210Folylpolyglutamate synthase0.500.311.411.44
    LBUL_0211Dihydropteroate synthase and related enzymes0.690.391.392.30
    LBUL_0212NTP pyrophosphohydrolases including oxidative damage repair enzymes0.630.311.262.88
    LBUL_0660Folylpolyglutamate synthase0.690.370.784.82
Purine metabolism
    LBUL_0156Phosphoribosylpyrophosphate synthetase2.091.160.440.50
    LBUL_0246IMP dehydrogenase/GMP reductase0.240.301.270.05
    LBUL_0251IMP dehydrogenase/GMP reductase2.630.681.330.91
    LBUL_0252GMP synthase PP-ATPase domain/subunit2.320.941.571.60
    LBUL_0305Phosphoribosylpyrophosphate synthetase0.780.660.571.32
    LBUL_1330Phosphoribosylamine-glycine ligase0.990.371.180.06
    LBUL_1331AICAR transformylase/IMP cyclohydrolase PurH (only IMP cyclohydrolase domain in Aful)1.210.431.230.05
    LBUL_1332Folate-dependent phosphoribosylglycinamide formyltransferase PurN1.200.581.220.06
    LBUL_1333Phosphoribosylaminoimidazole (AIR) synthetase1.290.341.190.04
    LBUL_1334Glutamine phosphoribosylpyrophosphate amidotransferase1.250.371.280.05
    LBUL_1335Phosphoribosylformylglycinamidine (FGAM) synthase synthetase domain1.660.461.180.07
    LBUL_1336Phosphoribosylformylglycinamidine (FGAM) synthase glutamine amidotransferase domain0.960.440.920.04
    LBUL_1337Phosphoribosylformylglycinamidine (FGAM) synthase PurS component0.890.610.810.03
    LBUL_1338Phosphoribosylaminoimidazolesuccinocarboxamide (SAICAR) synthase0.830.640.880.03
    LBUL_1339Adenylosuccinate lyase1.791.780.850.17
    LBUL_1340Phosphoribosylaminoimidazole carboxylase (NCAIR synthetase)2.051.900.920.10
    LBUL_1341Phosphoribosylcarboxyaminoimidazole (NCAIR) mutase1.961.550.570.14
    LBUL_1754GMP synthase-glutamine amidotransferase domain1.210.591.521.78
    str0030purCPhosphoribosylaminoimidazole-succinocarboxamide synthase2.741.150.270.10
    str0031purLPhosphoribosylformylglycinamidine synthase II (FGAM synthetase)1.941.500.400.31
    str0031purLPhosphoribosylformylglycinamidine synthase II (FGAM synthetase)1.941.500.400.31
    str0032purFAmidophosphoribosyltransferase1.591.610.450.43
    str0033purMPhosphoribosylaminoimidazole synthetase1.541.640.480.47
    str0034purNPhosphoribosylglycinamide formyltransferase1.471.600.500.48
    str0035purHBifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase1.862.180.470.70
    str0040purDPhosphoribosylamine-glycine ligase4.902.560.500.15
    str0041purEPhosphoribosylaminoimidazole carboxylase catalytic subunit5.764.050.790.20
    str0042purKPhosphoribosylaminoimidazole carboxylase5.413.900.770.31
    str0045purB1Adenylosuccinate lyase2.232.080.530.37
    str1640pflAPyruvate-formate lyase activating enzyme4.060.790.660.47
    str1657pflPyruvate formate-lyase3.031.380.970.76
BCAA metabolism
    LBUL_0077l-2-Hydroxyisocaproate dehydrogenase0.640.861.781.48
    LBUL_0392Aspartate/tyrosine/aromatic aminotransferase1.331.023.310.62
    LBUL_0431Branched-chain amino acid permease0.710.582.341.44
    LBUL_0659Valyl-tRNA synthetase1.080.431.276.46
    LBUL_0681Isoleucyl-tRNA synthetase0.940.621.744.51
    LBUL_1180Aspartate/tyrosine/aromatic aminotransferase1.151.210.511.13
    LBUL_1219BCAA aminotransferase/4-amino-4-deoxychorismate lyase0.640.630.564.74
    LBUL_1451Leucyl-tRNA synthetase0.860.410.873.54
    LBUL_2034Thiamine pyrophosphate-requiring enzymes [acetolactate synthase pyruvate dehydrogenase (cytochrome) glyoxylate carboligase phosphonopyruvate decarboxylase]0.440.240.8011.11
    str0220leuSLeucyl-tRNA synthetase2.131.952.171.22
    str0359livJBCAA ABC transporter substrate-binding protein1.370.801.300.60
    str0360livHBCAA ABC transporter permease protein1.180.761.330.79
    str0361livMBCAA ABC transporter permease protein1.090.671.341.22
    str0362livGBCAA ABC transporter ATP binding protein2.001.141.031.49
    str0363livFBCAA ABC transporter ATP binding protein1.510.620.961.37
    str0477valSValyl-tRNA synthetase1.030.833.594.89
    str0590bcaTBCAA aminotransferase2.011.180.780.30
    str0644hdhLl-2-Hydroxyisocaproate dehydrogenase1.141.111.153.24
    str0741ileSIsoleucyl-tRNA synthetase0.810.862.182.63
    str1357brnQBCAA transport system II carrier protein0.510.591.440.28
    str1438amiF1Oligopeptide ABC transporter ATP-binding protein0.490.392.750.72
    str1439amiEOligopeptide ABC transporter ATP-binding protein0.610.232.460.62
    str1440amiDOligopeptide ABC transporter membrane-binding protein0.450.142.730.55
    str1441amiCOligopeptide ABC transporter membrane-binding protein0.500.302.790.39
    str1635codYTranscriptional repressor CodY1.010.760.591.02
Sulfur amino acid metabolism
    LBUL_0089Homoserine trans-succinylase0.610.460.760.21
    LBUL_0096Methionine synthase II (cobalamin-independent)2.660.842.711.24
    LBUL_0268Homocysteine/selenocysteine methylase (S-methylmethionine-dependent)2.480.793.030.93
    LBUL_0297Methionyl-tRNA synthetase1.810.911.112.24
    LBUL_0685Adenosyl homosysteine nucleosidase0.230.354.175.42
    LBUL_0686Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes0.410.341.145.14
    LBUL_1103Bifunctional PLP-dependent enzyme with beta-cystathionase and maltose regulon repressor activities0.320.751.541.97
    LBUL_1232Methionine synthase II (cobalamin-independent)0.500.550.942.23
    LBUL_1235Cysteine synthase9.112.8823.092.84
    LBUL_1236Cystathionine beta-lyases/cystathionine gamma-synthases6.302.8513.944.31
    LBUL_1259Homoserine dehydrogenase0.930.931.841.02
    LBUL_1353Homoserine trans-succinylase0.500.270.590.08
    LBUL_1354Cysteine synthase0.690.210.360.03
    LBUL_1455S-Adenosylmethionine synthetase1.080.681.980.63
    LBUL_1554Cysteinyl-tRNA synthetase0.530.750.351.30
    str0083cysE1Serine acetyltransferase0.690.761.590.56
    str0084cysSCysteinyl-tRNA synthetase0.790.741.860.73
    str0352metB1Cystathionine gamma-synthase0.090.021.270.05
    str0366cysM1Cysteine synthase0.440.100.880.31
    str0451metGMethionine-tRNA ligase1.120.831.330.37
    str0566pfs5′-Methylthioadenosine/S-adenosylhomocysteine nucleosidase0.490.942.911.59
    str0584mmuMHomocysteine methyltransferase0.400.451.420.32
    str0846cysM2Cysteine synthase1.730.691.560.42
    str0847metB2Cystathionine beta-lyase1.170.680.910.86
    str0848cysE2Serine acetyltransferase, putative1.480.611.531.13
    str0987cysDO-Acetylhomoserine sulfhydrylase0.280.203.240.09
    str1172metKS-Adenosylmethionine synthetase0.400.571.520.06
    str1222metAHomoserine O-succinyltransferase0.280.261.490.13
Other amino acid and carbon dioxide metabolism
    LBUL_1105Subtilisin-like serine protease prtB0.450.428.890.42
    str1658cahCarbonate dehydratase15.753.730.710.92
ROS production and iron metabolism
    LBUL_2034Acetolactate synthase pyruvate dehydrogenase, (cytochrome) glyoxylate carboligase phosphonopyruvate decarboxylase0.440.240.8011.11
    LBUL_1241Translation initiation factor 2 (IF-2; GTPase)2.292.193.481.22
    LBUL_1955Dihydroorotate dehydrogenase0.941.042.601.10
    str1025fatBFerrichrome ABC transporter, substrate-binding protein0.830.904.340.59
    str1026fatAFerrichrome ABC transporter, ATP-binding protein0.661.004.520.54
    str1027fatCFerrichrome ABC transporter, permease protein0.740.963.950.34
    str1028fatDFerrichrome ABC transporter, permease protein0.770.952.740.09
    str0723dprPeroxide resistance protein, non-heme iron-containing ferritin1.480.760.351.22
    str0724furFerric transport regulator protein1.371.130.421.51
Fatty acid metabolism
    LBUL_01061-Acyl-sn-glycerol-3-phosphate acyltransferase1.370.533.131.40
    LBUL_01091-Acyl-sn-glycerol-3-phosphate acyltransferase0.630.624.760.91
    LBUL_0314Phosphopantetheinyl transferase (holo-ACP synthase)0.860.730.660.99
    LBUL_08183-Oxoacyl-(acyl-carrier-protein)1.670.370.260.20
    LBUL_0819Acyl carrier protein1.490.840.320.41
    LBUL_0820(Acyl-carrier-protein) S-malonyltransferase1.440.280.190.27
    LBUL_0821Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases)1.660.330.260.20
    LBUL_08223-Oxoacyl-(acyl-carrier-protein) synthase1.680.330.220.22
    LBUL_0823Biotin carboxyl carrier protein0.970.410.210.34
    LBUL_08243-Hydroxymyristoyl/3-hydroxydecanoyl-(acyl carrier protein) dehydratases1.270.290.290.47
    LBUL_0825Acetyl/propionyl-CoAb carboxylase alpha subunit0.980.300.130.39
    LBUL_0826Acetyl-CoA carboxylase beta subunit0.940.280.240.28
    LBUL_0827Acetyl-CoA carboxylase alpha subunit1.360.260.600.37
    LBUL_0828Enoyl-(acyl-carrier-protein)0.900.300.100.32
    LBUL_0829Biotin-(acetyl-CoA carboxylase) ligase0.790.260.300.28
    LBUL_12561-Acyl-sn-glycerol-3-phosphate acyltransferase1.090.351.5514.99
    LBUL_1294Acyl carrier protein0.881.000.291.78
    LBUL_1356Cyclopropane fatty acid synthase and related methyltransferases0.770.410.520.05
    LBUL_1567Biotin carboxylase1.640.983.590.76
    LBUL_1568Biotin carboxylase0.880.491.290.36
    LBUL_16073-Hydroxymyristoyl/3-hydroxydecanoyl-(acyl carrier protein) dehydratases0.600.440.714.36
  • a Numbers indicate the ratios of differential expression of a gene in the mixed culture compared to the monoculture. Numbers in boldface have a ratio >2 or <0.5 and are significant (P = 0.05).

  • b CoA, coenzyme A.