TABLE 4.

Examples of differentially regulateda genes in acid-adapted L. casei ATCC 334

General functional category and gene IDcPredicted functionFold change vs controlb
AA5AA20AA20-AC
Metabolism
    Energy production and conversion
        LSEI_0740Malolactic enzyme16.067.35NS
        LSEI_0741Malate/lactate antiporterNS5.99NS
        LSEI_1161ATP synthase C chain (EC 3.6.3.14)NS−5.00NS
    Carbohydrate transport, metabolism: LSEI_2764sn-Glycerol-3-phosphate transport system permease protein UgpANS2.71NS
    Amino acid transport, metabolism
        LSEI_2061Oligopeptide transport ATP-binding protein OppFNS3.27NS
        LSEI_2062Oligopeptide transport ATP-binding protein OppDNS5.49NS
        LSEI_2063Oligopeptide transport system permease protein OppCNS3.06NS
        LSEI_2064Oligopeptide transport system permease protein OppBNS3.39NS
        LSEI_0175Oligopeptide-binding protein OppANS3.64NS
        LSEI_1890Oligopeptide transport system permease protein OppBNS2.34NS
        LSEI_0046Branched-chain amino acid transport protein AzlDNS3.01NS
        LSEI_1260Histidine transport system permease protein HisMNS2.17NS
        LSEI_1426Histidinol-phosphate aminotransferase (2.6.1.9)NS7.52NS
        LSEI_1427Phosphoribosyl-ATP pyrophosphatase (EC 3.6.1.31)NS4.76NS
        LSEI_1429Imidazole glycerol phosphate synthase, cyclase subunit (EC 4.1.3.-)NS7.01NS
        LSEI_14301-(5-Phosphoribosyl)-5-[(5-phosphoribosylamino) methylideneamino]imidazole-4-carboxamide isomerase (EC 5.3.1.16)NS3.61NS
        LSEI_1431Imidazole glycerol phosphate synthase, glutamine amidotransferase subunit (EC 2.4.2.-)NS5.43NS
        LSEI_1432Imidazoleglycerol-phosphate dehydratase (EC 4.2.1.19)NS3.98NS
        LSEI_1433Histidinol dehydrogenase (EC 1.1.1.23)NS4.72NS
        LSEI_1434ATP phosphoribosyltransferase (EC 2.4.2.17)NS5.00NS
        LSEI_0078Anthranilate phosphoribosyltransferase (EC 2.4.2.18)NS2.68NS
        LSEI_0098Diaminopimelate decarboxylase (EC 4.1.1.20)NS2.803.01
        LSEI_2796Acetylornithine deacetylase (EC 3.5.1.16)/succinyl-diaminopimelate desuccinylase (EC 3.5.1.18), related deacylasesNS2.36NS
        LSEI_1345Arginine transport ATP-binding protein ArtPNS−3.00−3.83
        LSEI_1486Aspartate aminotransferase (EC 2.6.1.1)NS−3.21NS
        LSEI_1643Xaa-Pro dipeptidase (EC 3.4.13.9)NS−3.23NS
        LSEI_1652Glutamine synthetase (EC 6.3.1.2)NS−4.47NS
        LSEI_1653Transcriptional regulator, MerR familyNS−5.52NS
        LSEI_12885′-Methylthioadenosine nucleosidase (EC 3.2.2.16)/ S-adenosylhomocysteine nucleosidase (EC 3.2.2.9)NS−4.54−4.40
    Nucleotide transport and metabolism
        LSEI_1557Adenine phosphoribosyltransferase (EC 2.4.2.7)NS−3.19−3.26
        LSEI_1118Xanthine permeaseNS−3.16−4.12
        LSEI_1119Phosphoribosylaminoimidazole carboxylase NCAIR mutase subunit (EC 4.1.1.21)NS−3.33NS
        LSEI_1120Adenylosuccinate lyase (EC 4.3.2.2)NS−3.27−3.99
        LSEI_1286ADP-ribose pyrophosphatase (EC 3.6.1.13)−4.27−3.72−5.39
        LSEI_1746Phosphoribosylamine-glycine ligase (EC 6.3.4.13)NS−3.34NS
        LSEI_1747Phosphoribosylaminoimidazolecarboxamide formyltransferase (EC 2.1.2.3)/IMP cyclohydrolase (EC 3.5.4.10)NS−9.35−8.18
        LSEI_1748Phosphoribosylglycinamide formyltransferase (EC 2.1.2.2)NS−5.18NS
        LSEI_1749Phosphoribosylformylglycinamidine cycloligase (EC 6.3.3.1)NS−4.32−4.65
        LSEI_1750Amidophosphoribosyltransferase (EC 2.4.2.14)NS−4.48NS
        LSEI_1751Phosphoribosylformylglycinamidine synthase (EC 6.3.5.3)NS−4.47NS
        LSEI_1752Phosphoribosylformylglycinamidine synthase (EC 6.3.5.3)NS−4.75−4.77
        LSEI_1753Phosphoribosylformylglycinamidine synthase, PurS component (EC 6.3.5.3)−5.71−7.49−8.75
        LSEI_1754Phosphoribosylamidoimidazole-succinocarboxamide synthase (EC 6.3.2.6)NS−7.16−6.86
        LSEI_1755Phosphoribosylaminoimidazole carboxylase NCAIR mutase subunit (EC 4.1.1.21)NS−6.98−7.55
        LSEI_1756Phosphoribosylaminoimidazole carboxyltransferase subunit (EC 4.1.1.21)−5.09−7.49−8.35
        LSEI_1979GMP synthase (glutamine hydrolyzing) (EC 6.3.5.2)NS−3.82NS
        LSEI_1468Ribonucleoside-diphosphate reductase alpha chain (EC 1.17.4.1)NS−3.44NS
        LSEI_2482Adenylate kinase (EC 2.7.4.3)/nucleoside-diphosphate kinase (EC 2.7.4.6)NS−10.06NS
        LSEI_1450Orotidine 5′-phosphate decarboxylase (EC 4.1.1.23)NS−2.61−3.08
        LSEI_1806Nicotinate phosphoribosyltransferase (EC 2.4.2.11)NS−2.80−3.46
        LSEI_1378Cytidylate kinase (EC 2.7.4.14)NS−3.13NS
        LSEI_1669Uridine kinase (EC 2.7.1.48)−4.10−3.16−4.59
        LSEI_1668Transcription elongation factorNS−5.27NS
        LSEI_1159Uracil phosphoribosyltransferase (EC 2.4.2.9)NS−3.29NS
        LSEI_1584Uridylate kinaseNS−4.94NS
Information storage and processing
    Translation, ribosomal structure and biogenesis
        LSEI_0977tmRNA-binding proteinNS−2.62NS
        LSEI_1057Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit C (EC 6.3.5.-)NS−3.32NS
        LSEI_1058Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit A (EC 6.3.5.-)NS-3.24NS
        LSEI_1292tRNA (5-methylaminomethyl-2-thiouridylate)methyltransferase (EC 2.1.1.61)NS−4.24−4.78
        LSEI_1579Prolyl-tRNA synthetase (EC 6.1.1.15)NS−2.96NS
        LSEI_1280Isoleucyl-tRNA synthetase (EC 6.1.1.5)NS−2.97NS
        LSEI_1485Asparaginyl-tRNA synthetase (EC 6.1.1.22)NS−3.37NS
        LSEI_1703Threonyl-tRNA synthetase (EC 6.1.1.3)NS−3.80NS
        LSEI_0883Leucyl-tRNA synthetase (EC 6.1.1.4)NS−4.05NS
        LSEI_2569LSUd ribosomal protein L31PNS−2.78NS
        LSEI_1697LSU ribosomal protein L20PNS−4.60NS
        LSEI_1642Protein translation elongation factor P (EF-P)NS−5.55NS
        LSEI_1641General stress protein, Gls24 familyNS−5.18NS
        LSEI_1640Transcription antitermination factorNS−4.38NS
        LSEI_1644LSU ribosomal protein L27PNS−5.09NS
        LSEI_1645Hypothetical ribosome-associated proteinNS−8.30NS
        LSEI_1847LSU ribosomal protein L33PNS−6.38NS
        LSEI_1572Ribosome-binding factorNS−6.49NS
        LSEI_1573Protein translation initiation factor 2 (IF-2)NS−4.76NS
        LSEI_1574LSU ribosomal protein L7AE−7.33−7.55−5.64
        LSEI_1575Hypothetical cytosolic proteinNS−4.91NS
        LSEI_1576Transcription termination factorNS−3.88NS
        LSEI_1577Hypothetical cytosolic proteinNS−3.84NS
        LSEI_2272LSU ribosomal protein L12P (L7/L12)NS−13.08NS
        LSEI_2273LSU ribosomal protein L10PNS−10.70NS
        LSEI_2476LSU ribosomal protein L17PNS−7.52NS
        LSEI_2478SSUe ribosomal protein S11PNS−6.88NS
        LSEI_2479SSU ribosomal protein S13PNS−10.19NS
        LSEI_2480LSU ribosomal protein L36PNS−19.62NS
        LSEI_2481Protein translation initiation factor 1 (IF-1)NS−9.48NS
        LSEI_2484LSU ribosomal protein L15PNS−11.94NS
        LSEI_2485LSU ribosomal protein L30PNS−9.30NS
        LSEI_2486SSU ribosomal protein S5PNS−8.51NS
        LSEI_2487LSU ribosomal protein L18PNS−12.10NS
        LSEI_2488LSU ribosomal protein L6PNS−8.62NS
        LSEI_2489SSU ribosomal protein S8PNS−12.20NS
        LSEI_2490SSU ribosomal protein S14PNS−12.31NS
        LSEI_2491LSU ribosomal protein L5PNS−7.17NS
        LSEI_2492LSU ribosomal protein L24P−7.42−17.81NS
        LSEI_2493LSU ribosomal protein L14PNS−10.32NS
        LSEI_2494SSU ribosomal protein S17PNS−14.50NS
        LSEI_2495LSU ribosomal protein L29PNS−9.62NS
        LSEI_2496LSU ribosomal protein L16PNS−8.59NS
        LSEI_2497SSU ribosomal protein S3PNS−8.83NS
        LSEI_2499SSU ribosomal protein S19PNS−7.34NS
        LSEI_250050S ribosomal protein L2NS−7.79NS
        LSEI_2501LSU ribosomal protein L23PNS−9.67NS
        LSEI_2502LSU ribosomal protein L1E (= L4P)NS−6.11NS
        LSEI_2503Ribosomal protein L3NS−5.57NS
        LSEI_2508Protein translation elongation factor G (EF-G)NS−3.38NS
        LSEI_2509SSU ribosomal protein S7PNS−7.19NS
        LSEI_1379SSU ribosomal protein S1PNS−6.04NS
        LSEI_1244SSU ribosomal protein S4PNS−7.14NS
        LSEI_1601SSU ribosomal protein S16PNS−14.28NS
        LSEI_1327SSU ribosomal protein S20PNS−15.68NS
        LSEI_1328SSU ribosomal protein S15PNS−4.43NS
        LSEI_1332Protein translation elongation factor Tu (EF-TU)NS−8.07NS
        LSEI_0009SSU ribosomal protein S6PNS−8.45NS
        LSEI_1583Ribosome recycling factor (RRF)NS−5.90NS
        LSEI_1585Protein translation elongation factor TsNS−8.36NS
        LSEI_158630S ribosomal protein S2NS−13.17−7.52
        LSEI_1303Peptide deformylase (EC 3.5.1.88)NS−2.65NS
        LSEI_1393Peptide methionine sulfoxide reductase MsrA (EC 1.8.4.11)NS−3.02NS
    Mobile DNA elements
        LSEI_1333Transposase (transposase_12 superfamily)NS3.79NS
        LSEI_1101Transposase (transposase_12 superfamily)NS3.20NS
        LSEI_1103Transposase (transposase_12 superfamily)NS3.62NS
        LSEI_2689Transposase, IS30 familyNS2.43NS
        LSEI_2691Transposase, IS30 familyNS3.58NS
        LSEI_2008Transposase, IS30 familyNS2.21NS
        LSEI_1907Transposase, IS3 familyNS3.423.57
        LSEI_0597Transposase, IS3 familyNS3.03NS
        LSEI_0590Transposase, IS3 familyNS2.65NS
        LSEI_0580Transposase, IS5 familyNS3.37NS
        LSEI_0230Transposase, IS5 familyNS2.28NS
        LSEI_2166Transposase, IS66 familyNS2.56NS
        LSEI_0787ResolvaseNS−3.32NS
Cellular processes
    Protein turnover, stress response
        LSEI_1617General stress protein, Gls24 familyNS−2.45NS
        LSEI_1281Cold shock protein−3.71−2.80−3.52
        LSEI_1848Superoxide dismutase (EC 1.15.1.1)NS−3.64NS
        LSEI_0963ATP-dependent endopeptidase Clp proteolytic subunit ClpP (EC 3.4.21.92)NS−3.67NS
        LSEI_1467GlutaredoxinNS−5.19NS
        LSEI_1762ATP-dependent endopeptidase Clp ATP-binding subunit ClpE−5.54−6.19−5.08
        LSEI_1338FKBP-type peptidyl-prolyl cis-trans isomerase (trigger factor) (EC 5.2.1.8)NS−9.26NS
        LSEI_2239Chaperonin GroESNS−29.35NS
        LSEI_223860-kDa chaperonin GroELNS−8.56NS
        LSEI_1567Heat-inducible transcription repressor HrcANS−8.73−6.61
        LSEI_1566Molecular chaperone GrpENS−16.72−11.27
        LSEI_1565Molecular chaperone DnaKNS−13.71NS
        LSEI_1564Small hypothetical protein−14.36−12.59−9.71
        LSEI_1563Chaperone protein DnaJNS−5.22NS
    Signal transduction
        LSEI_2868Sensor kinase DpiB (EC 2.7.3.-)NS3.24NS
        LSEI_0460Two-component RRNS2.71NS
        LSEI_1679CsrR-like RRNS−2.77NS
    Cell envelope biogenesis
        LSEI_1033Glycosyltransferase family 8NS−2.54NS
        LSEI_1808N-Acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25)NS−2.85NS
        LSEI_2012dTDP-4-dehydrorhamnose reductase (EC 1.1.1.133)NS−3.00NS
        LSEI_2014dTDP-4-dehydrorhamnose 3,5-epimerase (EC 5.1.3.13)NS−2.90NS
        LSEI_2015Glucose-1-phosphate thymidylyltransferase (EC 2.7.7.24)NS−2.74NS
        LSEI_1117Xanthine phosphoribosyltransferase (EC 2.4.2.-)NS−3.04NS
        LSEI_1395Carboxy-terminal processing protease precursor (EC 3.4.21.102)NS−3.80NS
        LSEI_0796d-Alanyl carrier proteinNS−4.53−5.63
        LSEI_0797d-Alanyl transfer protein DltD precursorNS−4.07NS
        LSEI_0020Cell wall hydrolase (amidase family)NS−5.57NS
        LSEI_2029Cell wall hydrolase (amidase family)−5.54−11.28−12.11
    Cell division and chromosome partitioning
        LSEI_2441CrcB family proteinNS2.47NS
        LSEI_2442CrcB family proteinNS2.41NS
        LSEI_0932Cell division protein FtsXNS−2.58NS
        LSEI_1268Cell division protein FtsLNS−2.66NS
        LSEI_1274Cell division protein FtsANS−2.46NS
        LSEI_1275Cell division protein FtsZNS−4.89NS
        LSEI_1279Cell division initiation protein DivIVANS−4.27NS
        LSEI_1478Cell division initiation protein DivIVANS−7.37−9.28
        LSEI_0931Cell division ATP-binding protein FtsENS−4.89NS
Poorly characterized, general function prediction only
        LSEI_1868Acetyltransferase, GNAT familyNS2.85NS
        LSEI_2773EsteraseNS2.64NS
        LSEI_0140Putative membrane-associated phospholipid phosphataseNS2.57NS
  • a P < 0.05.

  • b Fold change in normalized microarray signal intensity represents the average value calculated from four independent replicates. Control, cells grown at pH 6.0; AA5 or AA20, cells grown at pH 6.0 and then acid adapted for 5 or 20 min, respectively, in fresh MRS adjusted to pH 4.5; AA20-AC, cells grown at pH 6.0, incubated for 20 min in MRS adjusted to pH 4.5, and then suspended in MRS at pH 2.0 for 10 min.

  • c Gene ID represents the locus tag used in GenBank for chromosomal or plasmid-carried genes in L. casei ATCC 334 (NC 008526 and NC 008502, respectively).

  • d LSU, large subunit.

  • e SSU, small subunit.