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 protein 0.36 0.47 0.57
    LBA0112 putative ABC transporter (glutamine), substrate-binding protein 0.53 0.71 0.83
    LBA0197 ABC transporter, oligopeptide-binding protein oppA1 6.22 4.43 1.92
    LBA0198 ABC transporter, oligopeptide-binding protein oppA1B 7.42 1.96 1.59
    LBA0200 ABC transporter, oligopeptide permease protein oppB1 6.70 6.31 1.67
    LBA0201 ABC transporter, oligopeptide permease protein oppC1 7.27 8.09 2.55
    LBA0202 oligopeptide ABC transporter, ATP-binding protein oppD1 7.44 7.09 3.89
    LBA0203 oligopeptide ABC transporter, ATP-binding protein oppF1 8.01 7.10 5.57
    LBA0849 diaminopimelate epimerase1.30 2.15 0.91
    LBA0850 aspartokinase/homoserine dehydrogenase1.33 1.89 0.79
    LBA0911 aminopeptidase pepC1.79 1.79 0.72
    LBA0943 cationic amino acid transporter2.94 2.90 1.51
    LBA1042 ABC transporter (glutamine) membrane-spanning permease0.93 0.44 0.71
    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 protein0.84 0.43 0.71
    LBA1080 putative methionine synthase metK 6.96 5.51 4.32
    LBA1086 amino acid permease 3.44 1.73 1.64
    LBA1135 macrolide efflux protein1.12 2.00 1.21
    LBA1211 homoserine kinase khsE1.841.671.32
    LBA1212 homoserine dehydrogenase hdh 2.25 1.501.20
    LBA1300 oligopeptide ABC transporter, substrate-binding protein oppA2 0.35 0.47 0.36
    LBA1301 oligopeptide ABC transporter, substrate-binding protein oppA2B 4.92 1.741.37
    LBA1302 oligopeptide ABC transporter, permease protein oppC21.292.141.43
    LBA1303 ABC transporter, oligopeptide permease protein oppB21.50 1.98 1.49
    LBA1305 oligopeptide ABC transporter, ATP-binding protein oppF21.50 2.00 1.33
    LBA1306 oligopeptide ABC transporter, ATP-binding protein oppD21.24 2.22 1.35
    LBA1341 branched-chain amino acid aminotransferase ILVE 2.13 1.081.26
    LBA1515 peptidase T pepT2.26 2.05 1.32
    LBA1665 oligopeptide ABC transporter, substrate-binding protein0.38 0.15 0.58
    LBA1837 cytosol nonspecific dipeptidase pepD/A1.031.55 3.10
    LBA1961 oligopeptide ABC transporter, substrate-binding protein 2.05 1.91 1.08
Carbohydrate transport and metabolism [G]
    LBA0600 xylulose-5-phosphate/fructose phosphoketolase1.31 3.22 0.78
    LBA1467 beta-galactosidase large subunit (lactase) 0.07 0.17 0.27
    LBA1468 beta-galactosidase small subunit 0.17 0.43 1.05
    LBA1777 PTS system, fructose-specific enzyme II0.981.26 0.41
    LBA1778 fructose-1-phosphate kinase1.001.30 0.29
    LBA1779 transcriptional repressor (fructose operon)0.921.32 0.35
    LBA1870 maltose phosphorylase 0.67 0.90 0.21
    LBA1872 oligo-1,6-glucosidase0.970.88 0.46
Inorganic ion transport and metabolism [P]
    LBA0319 ABC transporter, ATP-binding protein1.191.061.88
    LBA0320 ABC transporter, ATP-binding protein1.250.87 1.96
    LBA0321 ABC transporter, permease protein1.341.33 2.21
    LBA0904 outer membrane lipoprotein precursor2.11 2.11 1.19
    LBA0905 ABC transporter, ATP-binding protein2.08 2.07 1.40
    LBA0906 ABC transporter, permease protein1.99 2.88 2.19
    LBA1683 cation-transporting ATPase 7.95 1.921.83
Signal transduction mechanisms [T]
    LBA0149 hypothetical protein1.281.01 0.56
    LBA0403 hypothetical protein1.011.301.21
    LBA1081 autoinducer-2 production protein luxS1.69 2.27 1.51
    LBA1524 two-component sensor histidine kinase1.17 2.82 0.97
    LBA1525 two-component system regulator 2.09 1.54 1.03
Defense mechanisms [V]
    LBA0074 ABC transporter, ATP-binding and permease protein 2.27 0.961.07
    LBA0075 ABC transporter, ATP-binding and permease protein 3.01 3.90 2.94
    LBA1838 ABC transporter, ATP-binding protein1.55 4.15 7.37
    LBA1839 putative permease1.48 5.16 8.72
    LBA1876 ABC transporter, ATP-binding/membrane-spanning protein1.79 1.98 1.59
Posttranslational modification, protein turnover, chaperones [O]
    LBA0165 neutral endopeptidase pepO 2.91 3.28 1.97
    LBA1512 proteinase P precursor prtP 7.53 7.02 1.58
    LBA1564 putative membrane protein1.42 1.47 2.08
Cell wall/membrane/envelope biogenesis [M]
    LBA0018 unknown0.901.00 0.55
    LBA1469 UDP-glucose 4-epimerase 0.18 0.510.67
Transcription [K]
    LBA1840 transcriptional regulator (TetR/AcrR family)1.33 3.52 12.60
General function prediction only [R]
    LBA0367 putative receptor1.04 1.74 1.26
Energy production and conversion [C]
    LBA0463 acetate kinase 2.31 1.121.27
Translation, ribosomal structure, and biogenesis [J]
    LBA0672 putative phosphate starvation induced protein yvyD1.120.93 0.43
Intracellular trafficking, secretion, and vesicular transport [U]
    LBA1496 putative fibrinogen-binding protein 3.56 2.35 1.22
Replication, recombination, and repair [L]
    LBA1565 unknown2.021.431.37
Function unknown/general function prediction only [S], [R]
    LBA0555 myosin-crossreactive antigen1.050.98 0.43
    LBA0872 putative membrane protein2.14 5.27 2.97
    LBA1119 putative inner membrane protein 4.22 3.46 6.24
    LBA1869 beta-phosphoglucomutase0.690.70 0.24
    LBA1952 hypothetical protein1.070.89 2.26
No COG found
    LBA0352 hypothetical protein0.940.87 0.47
    LBA0402 unknown1.010.811.38
    LBA0404 hypothetical protein0.88 0.60 0.95
    LBA1495 putative fibrinogen-binding protein1.620.971.15
    LBA1611 surface protein fmtB 0.56 0.930.94
    LBA1690 putative membrane protein1.621.32 2.34
  • 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).