TABLE 2.

ORFs differentially expressed in the HPK mutant (NCK1686) compared to the control L. acidophilus NCK1398 (NCFM::lacL) under different pH conditionsa

COGb functional classification/geneRelative mRNA ratio (HPK/WT)c
pH 6.8pH 5.5pH 4.5
Amino acid transport and metabolism [E]
    LBA0111 putative ABC transporter (glutamine), ATP-binding protein0.360.470.57
    LBA0112 putative ABC transporter (glutamine), substrate-binding protein0.530.710.83
    LBA0197 ABC transporter, oligopeptide-binding protein oppA16.224.431.92
    LBA0198 ABC transporter, oligopeptide-binding protein oppA1B7.421.961.59
    LBA0200 ABC transporter, oligopeptide permease protein oppB16.706.311.67
    LBA0201 ABC transporter, oligopeptide permease protein oppC17.278.092.55
    LBA0202 oligopeptide ABC transporter, ATP-binding protein oppD17.447.093.89
    LBA0203 oligopeptide ABC transporter, ATP-binding protein oppF18.017.105.57
    LBA0849 diaminopimelate epimerase1.302.150.91
    LBA0850 aspartokinase/homoserine dehydrogenase1.331.890.79
    LBA0911 aminopeptidase pepC1.791.790.72
    LBA0943 cationic amino acid transporter2.942.901.51
    LBA1042 ABC transporter (glutamine) membrane-spanning permease0.930.440.71
    LBA1044 ABC transporter (glutamine) membrane-spanning permease0.910.470.72
    LBA1045 ABC transporter (glutamine) ATP-binding protein0.780.390.82
    LBA1046 ABC transporter (glutamine) substrate-binding protein0.840.430.71
    LBA1080 putative methionine synthase metK6.965.514.32
    LBA1086 amino acid permease3.441.731.64
    LBA1135 macrolide efflux protein1.122.001.21
    LBA1211 homoserine kinase khsE1.841.671.32
    LBA1212 homoserine dehydrogenase hdh2.251.501.20
    LBA1300 oligopeptide ABC transporter, substrate-binding protein oppA20.350.470.36
    LBA1301 oligopeptide ABC transporter, substrate-binding protein oppA2B4.921.741.37
    LBA1302 oligopeptide ABC transporter, permease protein oppC21.292.141.43
    LBA1303 ABC transporter, oligopeptide permease protein oppB21.501.981.49
    LBA1305 oligopeptide ABC transporter, ATP-binding protein oppF21.502.001.33
    LBA1306 oligopeptide ABC transporter, ATP-binding protein oppD21.242.221.35
    LBA1341 branched-chain amino acid aminotransferase ILVE2.131.081.26
    LBA1515 peptidase T pepT2.262.051.32
    LBA1665 oligopeptide ABC transporter, substrate-binding protein0.380.150.58
    LBA1837 cytosol nonspecific dipeptidase pepD/A1.031.553.10
    LBA1961 oligopeptide ABC transporter, substrate-binding protein2.051.911.08
Carbohydrate transport and metabolism [G]
    LBA0600 xylulose-5-phosphate/fructose phosphoketolase1.313.220.78
    LBA1467 beta-galactosidase large subunit (lactase)0.070.170.27
    LBA1468 beta-galactosidase small subunit0.170.431.05
    LBA1777 PTS system, fructose-specific enzyme II0.981.260.41
    LBA1778 fructose-1-phosphate kinase1.001.300.29
    LBA1779 transcriptional repressor (fructose operon)0.921.320.35
    LBA1870 maltose phosphorylase0.670.900.21
    LBA1872 oligo-1,6-glucosidase0.970.880.46
Inorganic ion transport and metabolism [P]
    LBA0319 ABC transporter, ATP-binding protein1.191.061.88
    LBA0320 ABC transporter, ATP-binding protein1.250.871.96
    LBA0321 ABC transporter, permease protein1.341.332.21
    LBA0904 outer membrane lipoprotein precursor2.112.111.19
    LBA0905 ABC transporter, ATP-binding protein2.082.071.40
    LBA0906 ABC transporter, permease protein1.992.882.19
    LBA1683 cation-transporting ATPase7.951.921.83
Signal transduction mechanisms [T]
    LBA0149 hypothetical protein1.281.010.56
    LBA0403 hypothetical protein1.011.301.21
    LBA1081 autoinducer-2 production protein luxS1.692.271.51
    LBA1524 two-component sensor histidine kinase1.172.820.97
    LBA1525 two-component system regulator2.091.541.03
Defense mechanisms [V]
    LBA0074 ABC transporter, ATP-binding and permease protein2.270.961.07
    LBA0075 ABC transporter, ATP-binding and permease protein3.013.902.94
    LBA1838 ABC transporter, ATP-binding protein1.554.157.37
    LBA1839 putative permease1.485.168.72
    LBA1876 ABC transporter, ATP-binding/membrane-spanning protein1.791.981.59
Posttranslational modification, protein turnover, chaperones [O]
    LBA0165 neutral endopeptidase pepO2.913.281.97
    LBA1512 proteinase P precursor prtP7.537.021.58
    LBA1564 putative membrane protein1.421.472.08
Cell wall/membrane/envelope biogenesis [M]
    LBA0018 unknown0.901.000.55
    LBA1469 UDP-glucose 4-epimerase0.180.510.67
Transcription [K]
    LBA1840 transcriptional regulator (TetR/AcrR family)1.333.5212.60
General function prediction only [R]
    LBA0367 putative receptor1.041.741.26
Energy production and conversion [C]
    LBA0463 acetate kinase2.311.121.27
Translation, ribosomal structure, and biogenesis [J]
    LBA0672 putative phosphate starvation induced protein yvyD1.120.930.43
Intracellular trafficking, secretion, and vesicular transport [U]
    LBA1496 putative fibrinogen-binding protein3.562.351.22
Replication, recombination, and repair [L]
    LBA1565 unknown2.021.431.37
Function unknown/general function prediction only [S], [R]
    LBA0555 myosin-crossreactive antigen1.050.980.43
    LBA0872 putative membrane protein2.145.272.97
    LBA1119 putative inner membrane protein4.223.466.24
    LBA1869 beta-phosphoglucomutase0.690.700.24
    LBA1952 hypothetical protein1.070.892.26
No COG found
    LBA0352 hypothetical protein0.940.870.47
    LBA0402 unknown1.010.811.38
    LBA0404 hypothetical protein0.880.600.95
    LBA1495 putative fibrinogen-binding protein1.620.971.15
    LBA1611 surface protein fmtB0.560.930.94
    LBA1690 putative membrane protein1.621.322.34
  • a Array ratios from two biological replicates and two technical replicates for each condition were averaged.

  • b COG, clusters of orthologous groups (37). Genes were classified according to the COG domain present in the potentially encoded protein sequence; letters in brackets are COG functional category codes.

  • c Values in boldface indicate ratios that meet the P criteria (P < 0.05).