TABLE 2.
Responses of L. lactis subsp. lactis IL1403 during different stress treatmentsa
| Function | Gene | Fold changeb with:
|
Description of gene productf | ||||
|---|---|---|---|---|---|---|---|
| Heatc | Acidd | Salte | |||||
| PTS | ptsH | −2.9 | Phosphocarrier protein Hpr | ||||
| ptsI | −2.2 | Phosphotransferase system, enzyme I (EC 2.7.3.9) | |||||
| yedE | −340.1 | −14.2 | PTS system, beta-glucosides-specific IIA component, putative (EC 2.7.1.69) | ||||
| yedF | −2.4 | −83.5 | −6.8 | Beta-glucoside-specific PTS system IIBC component (EC 2.7.1.69) | |||
| Sugar metabolism | pmi | −5.6 | Mannose-6-phosphate isomerase (EC 5.3.1.8) | ||||
| uxuB | +14.9 | Fructuronate reductase (EC 1.1.1.57) | |||||
| yrcA | −4.6 | −2.2 | Phospho-beta-glucosidase (EC 3.2.1.86) | ||||
| Glycolysis/gluconeogenesis | enoA | −2.2 | Enolase (EC 4.2.1.11) | ||||
| enoB | +3.3 | 2-Phosphoglycerate dehydratase (EC 4.2.1.11) | |||||
| fbp | −14.1 | −21.5 | Fructose-1,6-bisphosphatase (EC 3.1.3.11) | ||||
| gapB | −3.3 | −3.8 | Glyceraldehyde 3-phosphate dehydrogenase (EC 1.2.1.12) | ||||
| Pentose phosphate pathway | gnd | −5.2 | −3.6 | 6-Phosphogluconate dehydrogenase; decarboxylating (EC 1.1.1.44) | |||
| tkt | −2.6 | Transketolase (EC 2.2.1.1) | |||||
| zwf | +4.0 | Glucose-6-phosphate 1-dehydrogenase (EC 1.1.1.49) | |||||
| Pyruvate metabolism | citE | +2.8 | −14.7 | Citrate lyase beta chain (EC 4.1.3.6) | |||
| citF | +14.3 | Citrate lyase alpha chain (EC 4.1.3.6 2.8.3.10) | |||||
| ldh | −2.0 | +2.3 | l-lactate dehydrogenase (EC 1.1.1.27) | ||||
| mae | −9.7 | Malate oxidoreductase (EC 1.1.1.38) | |||||
| mleS | −30.6 | +2.9 | −2.8 | Malolactic enzyme (EC 1.1.1.38) | |||
| Fatty acid biosynthesis | accA | −3.2 | −30.8 | Acetyl-CoA carboxylase carboxyl transferase subunit alpha (EC 6.4.1.2) | |||
| accB | −4.7 | Acetyl-CoA carboxylase biotin carboxyl carrier protein | |||||
| accC | −51.2 | Biotin carboxylase (EC 6.3.4.14) | |||||
| fabD | −2.3 | Malonyl CoA-acyl carrier protein transacylase (EC 2.3.1.39) | |||||
| fabG1 | −3.7 | 3-Oxoacyl-[acyl-carrier protein] reductase (EC 1.1.1.100) | |||||
| fabH | −6.0 | 3-Oxoacyl-[acyl-carrier-protein] synthase III (EC 2.3.1.41) | |||||
| fabZ2 | −5.8 | (3R)-Hydroxymyristoyl-[acyl carrier protein] dehydratase (EC 4.2.1.-) | |||||
| Fatty acid catabolism | fadA | +4.2 | +24.7 | Acetyl coenzyme A acetyltransferase (EC 2.3.1.9) | |||
| lplL | −18.5 | Lipoate-protein ligase (EC 6.-.-.-) | |||||
| thiL | +3.8 | Acetyl coenzyme A acetyltransferase (EC 2.3.1.9) | |||||
| RNA polymerase | rpoE | +2.9 | DNA-directed RNA polymerase delta chain (EC 2.7.7.6) | ||||
| RNA reaction | truA | +19.1 | tRNA pseudouridine synthase A (EC 4.2.1.70) | ||||
| truB | +2.7 | tRNA pseudouridine synthase B (EC 4.2.1.70) | |||||
| yljE | +4.5 | Putative RNA methyltransferase (EC 2.1.1.-) | |||||
| Aminoacyl-tRNA biosynthesis | alaS | +5.7 | Alanyl-tRNA synthetase (EC 6.1.1.7) | ||||
| argS | +3.0 | Arginyl-tRNA synthetase (EC 6.1.1.19) | |||||
| fmt | +5.3 | Methyonyl-tRNA formyltransferase (EC 2.1.2.9) | |||||
| gatA | +2.9 | Glu-tRNA amidotransferase subunit A (EC 6.3.5.-) | |||||
| gltX | +3.5 | Glutamyl-tRNA synthetase (EC 6.1.1.17) | |||||
| glyT | −2.8 | −8.7 | Glycyl-tRNA synthetase beta chain (EC 6.1.1.14) | ||||
| ileS | −3.4 | −10.2 | Isoleucyl-tRNA synthetase (EC 6.1.1.5) | ||||
| leuS | +6.5 | Leucyl-tRNA synthetase (EC 6.1.1.4) | |||||
| Deoxyribonucleotide and ribonucleotide interconversions | nrdE | −9.0 | +4.1 | Ribonucleoside-diphosphate reductase alpha chain (EC 1.17.4.1) | |||
| nrdF | −7.8 | Ribonucleoside-diphosphate reductase beta chain (EC 1.17.4.1) | |||||
| Deoxyribonucleotide biosynthesis | dukA | +21.9 | +4.3 | +6.2 | Deoxypurine kinase (EC 2.7.1.113) | ||
| dut | +10.3 | Deoxyuridine 5′-triphosphate nucleotidhydrolase (EC 3.6.1.23) | |||||
| thyA | 2.8 | +5.7 | Thymidylate synthase (EC 2.1.1.45) | ||||
| yeaB | +14.7 | dTMP kinase (EC 2.7.4.9) | |||||
| Ribonucleotide biosynthesis | purA | −28.0 | Adenylosuccinate synthase (EC 6.3.4.4) | ||||
| purL | −6.6 | −24.9 | Phosphoribosylformylglycinamidine synthase II (EC 6.3.5.3) | ||||
| purN | +8.8 | Phosphoribosylglycinamide formyltransferase (EC 2.1.2.2) | |||||
| pydA | +4.5 | Dihydroorotate dehydrogenase A (EC 1.3.3.1) | |||||
| Salvage of nucleosides and nucleotides | add | +3.3 | −12.5 | Adenosine deaminase (EC 3.5.4.4) | |||
| deoB | −2.3 | +3.5 | Phosphopentomutase (EC 5.4.2.7) | ||||
| prsA | +2.4 | Ribose-phosphate pyrophosphokinase (EC 2.7.6.1) | |||||
| prsB | +8.2 | Ribose-phosphate pyrophosphokinase (EC 2.7.6.1) | |||||
| udp | +22.7 | Uridine phosphorylase (EC 2.4.2.3) | |||||
| upp | +4.9 | Uracil phosphoribosyltransferase (EC 2.4.2.9) | |||||
| yfiG | +9.4 | +6.4 | +6.2 | Thymidine kinase (EC 2.7.1.21) | |||
| Other ribonucleotide metabolism | pnpA | −7.8 | −4.0 | Polyribonucleotide nucleotidyltransferase (EC 2.7.7.8) | |||
| relA | +2.1 | GTP pyrophosphokinase (EC 2.7.6.5) | |||||
| ytfB | +9.9 | ADP-ribose pyrophosphatase (EC 3.6.1.13) | |||||
| Protease | yueE | +3.5 | Protease | ||||
| yuhB | +4.7 | Protease | |||||
| Peptidase | gcp | +4.4 | O-sialoglycoprotein endopeptidase (EC 3.4.24.57) | ||||
| pepC | −35.6 | Aminopeptidase C (EC 3.4.22.40) | |||||
| pepDA | +3.8 | Dipeptidase (EC 3.4.-.-) | |||||
| pepP | −7.8 | Aminopeptidase P (EC 3.4.11.9) | |||||
| pepXP | −4.6 | X-prolyl dipeptidyl aminopeptidase (EC 3.4.14.11) | |||||
| Peptide transporter | dtpT | −22.6 | −11.7 | Di-/tripeptide transporter | |||
| optB | −19.4 | −3.3 | −3.5 | Oligopeptide ABC transporter permease protein | |||
| optC | −17.5 | Oligopeptide ABC transporter permease protein | |||||
| optD | −23.3 | −5.6 | Oligopeptide ABC transporter ATP binding protein | ||||
| optF | −13.7 | −4.1 | −5.8 | Oligopeptide ABC transporter ATP binding protein | |||
| Aromatic amino acid biosynthesis | aroA | −6.4 | 3-Phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) | ||||
| aroD | +3.2 | 3-Dehydroquinate dehydratase (EC 4.2.1.10) | |||||
| Function | Gene | Fold changeb with:
|
Description of gene productf | ||||
| Heatc | Acidd | Salte | |||||
| aroF | +3.3 | Phospho-2-dehydro-3-deoxyheptonate aldolase (EC 4.1.2.15) | |||||
| trpF | +19.5 | Phosphorybosyl-anthranilate isomerase (EC 5.3.1.24) | |||||
| trpG | +6.1 | Anthranilate synthase component II (EC 4.1.3.27) | |||||
| Aspartate family amino acid biosynthesis | ansB | +16.6 | l-asparaginase (EC 3.5.1.1) | ||||
| asnH | +9.4 | Asparagine synthase (EC 6.3.5.4) | |||||
| dapA | +4.1 | Dihydrodipicolinate synthase (EC 4.2.1.52) | |||||
| dapB | +2.6 | Dihydrodipicolinate reductase (EC 1.3.1.26) | |||||
| hom | −3.6 | Homoserine dehydrogenase (EC 1.1.1.3) | |||||
| lysA | +2.4 | Diaminopimelate decarboxylase (EC 4.1.1.20) | |||||
| metA | +25.4 | Homoserine O-succinyltransferase (EC 2.3.1.46) | |||||
| metB1 | +24.0 | Cystathionine gamma-synthase (EC 4.2.99.9) | |||||
| metB2 | +5.7 | Cystathionine beta-lyase (EC 4.4.1.8) | |||||
| metE | −3.9 | 5-Methionine synthase (EC 2.1.1.14) | |||||
| thrC | −3.1 | Threonine synthase (EC 4.2.99.2) | |||||
| ychH | −8.4 | 2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase (EC 2.3.1.117) | |||||
| Branch chain amino acid biosynthesis | ilvC | +6.6 | Ketol acid reductoisomerase (EC 1.1.1.86) | ||||
| Glutamate family amino acid metabolism | glnA | −18.3 | −3.7 | Glutamine synthetase (EC 6.3.1.2) | |||
| gltB | +4.0 | Glutamate synthase (NADPH) large chain (EC 1.4.1.13) | |||||
| gltD | −2.8 | +2.7 | Glutamate synthase (NADPH) small chain (EC 1.4.1.13) | ||||
| Histidine biosynthesis | hisH | −6.3 | Amidotransferase (EC 2.4.2.-) | ||||
| Serine family amino acid biosynthesis | cysE | +5.5 | Serine acetyltransferase (EC 2.3.1.30) | ||||
| cysK | +5.1 | Cysteine synthase (EC 4.2.99.8) | |||||
| Amino acid catabolism | araT | −2.6 | Aromatic amino acid specific aminotransferase (EC 2.6.1.-) | ||||
| arcA | −6.5 | −61.1 | Arginine deiminase (EC 3.5.3.6) | ||||
| glmS | +10.3 | Glucosamine-fructose-6-phosphate aminotransferase (isomerizing) (EC 2.6.1.16) | |||||
| metK | +2.3 | S-adenosylmethionine synthetase (EC 2.5.1.6) | |||||
| sdaB | +6.0 | l-serine dehydratase beta subunit (EC 4.2.1.13) | |||||
| yeiG | +3.7 | Putative aminotransferase (EC 2.6.1.-) | |||||
| ytjE | +33.4 | Aminotransferase (EC 2.6.1.-) | |||||
| Amino acid transporter | arcD1 | −23.8 | Arginine/ornitine antiporter | ||||
| arcD2 | −3.1 | −2.4 | −2.9 | Arginine/ornitine antiporter | |||
| brnQ | −27.4 | Branch chain amino acid transporter | |||||
| glnP | −14.6 | −24.1 | Glutamine ABC transporter permease and substrate binding protein | ||||
| glnQ | −6.5 | −16.3 | Glutamine ABC transporter ATP-binding protein | ||||
| lysQ | −81.3 | Lysine-specific permease | |||||
| ydcC | +7.0 | Amino acid ABC transporter permease protein | |||||
| ydgC | +3.1 | Amino acid permease | |||||
| yjgC | +25.2 | Amino acid ABC transporter substrate binding protein | |||||
| yjgD | +4.5 | −6.1 | Amino acid ABC transporter permease protein | ||||
| yjgE | +86.8 | Amino acid ABC transporter ATP binding protein | |||||
| yvdF | +2.5 | Amino acid ABC transporter substrate binding protein | |||||
| ABC transporters, prokaryotic | busAA | +26.9 | +60.0 | Betaine ABC transporter ATP binding protein | |||
| busAB | +13.8 | +49.9 | Betaine ABC transporter permease and substrate binding protein | ||||
| choQ | +7.8 | Choline ABC transporter ATP binding protein | |||||
| choS | +24.7 | +2.5 | Choline ABC transporter permease and substrate binding protein | ||||
| potA | −2.6 | Spermidine/putrescine ABC transporter ATP-binding protein | |||||
| potB | −8.4 | Spermidine/putrescine ABC transporter permease protein | |||||
| Peptidoglycan and polysaccharide biosynthesis | dltA | +2.5 | d-alanine activating enzyme (EC 6.3.2.-) | ||||
| murF | +3.3 | UDP-N-acetylmuramoylalanyl-d-glutamyl-2,6-diaminopimelate-d-alanyl-d-alanyl ligase (EC 6.3.2.15) | |||||
| murG | +7.5 | UDP-N-acetylglucosamine-N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase (EC 2.4.1.-) | |||||
| murI | +3.7 | Glutamate racemase (EC 5.1.1.3) | |||||
| racD | −2.3 | Aspartate racemase (EC 5.1.1.13) | |||||
| Menaquinone and ubiquinone biosynthesis | hmcM | −10.7 | −3.3 | Hydroxymethylglutaryl-CoA synthase (EC 4.1.3.5) | |||
| menD | +4.7 | 2-Oxoglutarate decarboxylase/2-succinyl-6-hydroxy-2,4-Cyclohexadiene-1-carboxylate synthase (EC 4.1.1.71 4.1.3.-) | |||||
| yhdB | +17.2 | O-succinylbenzoate-CoA synthase (EC 4.2.1.-) | |||||
| yhfE | +44.2 | Hypothetical methlytransferase (EC 2.1.1.-) | |||||
| Glutathione and thioredoxin | gshR | +4.8 | Glutathione reductase (EC 1.6.4.2) | ||||
| trxB1 | +3.7 | Thioredoxin reductase (EC 1.6.4.5) | |||||
| One carbon pool by folate | folD | +2.7 | Methylenetetrahydrofolate dehydrogenase (NADP+)/methenyltetrahydrofolate cyclohydrolase (EC 1.5.1.5 3.5.4.9) | ||||
| Folic acid biosynthesis | pabA | −13.8 | para-aminobenzoate synthetase component II (EC 4.1.3.-) | ||||
| pabB | −8.0 | para-aminobenzoate synthase component I (EC 4.1.3.-) | |||||
| Heat shock protein | dnaK | +8.3 | +10.3 | DnaK protein | |||
a
The threshold for the software package SAM was minimal two-fold change in expression ratio and maximal false discovery rate of 1%.
b
An empty slot indicated no significant change between the control and the treatment. +, gene expression was induced under the stress condition than in control condition; −, gene expression was repressed under the stress condition.
c
In heat shock responses, the median number of genes whose expression was falsely called significant was 0.46, with a median false discovery rate of 0.72%. That is, on average we expected less than one false positive in this column.
d
In acid shock responses, the median number of genes whose expression was falsely called significant was 0.42, with a median false discovery rate of 0.85%. That is, on average we expected less than one false positive in this column.
e
In osmotic shock responses, the median number of genes whose expression was falsely called significant was 0.45, with a median false discovery rate of 0.66%. That is, on average we expected less than one false positive in this column.