TABLE 1.

Changes in S. thermophilus mRNA levels in coculture with L. delbrueckii subsp. bulgaricus between early and late exponential phases

Gene name or locus tag (stu no.)dFunctional categoryDescriptionFold change L vs EaPutative operon structureb
MicroarrayRT-qPCR
0158AA and peptide transporterPolar AA ABC transporter, ATP binding protein3.9stu0159-0158
0159Polar AA ABC transporter, permease2.4cstu0159-0158
0605Polar AA ABC transporter, permease4.6stu0605-0606
1579Polar AA ABC transporter, substrate binding protein2.7cstu1582-1581-1580-1579
1580Polar AA ABC transporter, ATP binding protein4.4stu1582-1581-1580-1579
1652Polar AA ABC transporter, ATP binding protein3.5stu1653-1652
1653Polar AA ABC transporter, permease3.9stu1653-1652
argRAA metabolismArginine repressor3.7argR-stu0049-mutS1
argCN-Acetyl-gamma-glutamyl-phosphate reductase2.7cargCJBD
argJBifunctional ornithine acetyltransferase/N-acetylglutamate synthase protein6.3argCJBD
argBAcetylglutamate kinase4.5argCJBD
argDAcetylornithine aminotranferase4.9argCJBD
ilvDDihydroxy-acid dehydratase3.0c2.0 ± 0.2ilvD
argHArginosuccinate lyase3.2c57.5 ± 10argH
ilvCKetol-acid reductoisomerase5.62.1 ± 0.4ilvC
ilvBAcetolactate synthase, large subunitNVNVilvBN
leuB3-Isopropylmalate dehydrogenaseNVNVleuAB
thrBHomoserine kinase2.8cthrB-rarD
aldBAlpha-acetolactate decarboxylaseNVNVals-aldB
1413Bifunctional glutamate-cysteine ligase6.6stu1413
0336Purine and pyrimidinePutative MFS transporter, xanthine/uracil permease2.4c1.8 ± 0.40stu0336
prsA1    metabolismRibose-phosphate pyrophosphokinase0.240.14 ± 0.05prsA1
purCPhosphoribosylaminoimidazole-succinocarboxamide synthase0.120.39 ± 0.10purCLFMNH
purLPhosphoribosylformylglycinamidine synthase II0.140.03 ± 0.01purCLFMNH
purFAmidophosphoribosyltransferase0.19purCLFMNH
purMPhosphoribosylformylglycinamide cyclo-ligase0.36cpurCLFMNH
purNPhosphoribosylformylglycinamide formyl transferase0.3cpurCLFMNH
purHPhosphoribosylaminoimidazole carboxamide formyl transferase0.26cpurCLFMNH
purDPhosphoribosylamine-glycine lyase0.3cpurDEK
purEPhosphoribosylaminoimidazole carboxylase I0.36cpurDEK
purBAdenylosuccinate lyase0.590.22 ± 0.08purB
purAAdenylosuccinate synthetaseNV0.40 ± 0.14purA
purRPurine operon repressorNV1.90 ± 0.40purR
pyrCDihydroorotase5.8ung-pyrC
feoAMetal ion metabolismFerrous iron uptake transporter, protein ANV0.33 ± 0.15feoABC
feoBFerrous iron uptake transporter, protein BNVfeoABC
feoCHypothetical proteinNP0.43 ± 0.2feoAB
mntHMn2+ transporter3.61.7 ± 0.2mntH
dprPeroxide resistance protein, non-heme-containing ferritin18.313.7 ± 4.0dpr-fur
furFerric transport regulator protein8.1dpr-fur
tatASec-independent protein translocaseNV0.14 ± 0.02stu1024-1023-1022-tatC-tatA
tatCSec-independent protein translocase0.4cstu1024-1023-1022-tatC-tatA
1022Predicted membrane protein of the lead (Pb2+) uptake porter (PbrT) family0.3stu1024-1023-1022-tatC-tatA
1023Hypothetical protein, putative iron-dependent peroxidase0.4cstu1024-1023-1022-tatC-tatA
1024Hypothetical protein (predicted lipoprotein)0.4cstu1024-1023-1022-tatC-tatA
fatBIron complex ABC transporter, substrate binding protein0.4cfatDCAB
fatAIron complex ABC transporter, ATP binding protein0.2fatDCAB
fatCIron complex ABC transporter, permease0.4cfatDCAB
hrcAStressHeat-inducible transcription repressorNV0.16 ± 0.07hrcA-grpE-dnaK
grpEHeat shock protein, chaperonine0.3hrcA-grpE-dnaK
dnaKMolecular chaperoneNVhrcA-grpE-dnaK
htpXHeat shock protein4.5htpX
htrAExported serine protease4htrA
0808C metabolismSimple sugar transport system, substrate-binding protein0.30.11 ± 0.01stu0806-0807-0808-0809- 0810-0811
manNMannose PTS system, component IID4.4manLMN-stu0330
manMMannose PTS system, component IICNVmanLMN-stu0330
manLMannose PTS system, component IIAB3.6manLMN-stu0330
mutS1DNA and RNA metabolismDNA mismatch repair protein2.4cargR-stu0049-mutS1
polCDNA polymerase III5.0polC
ungUracyl DNA glycosylase8.7ung-pyrC
rheATP-dependent RNA helicase6.0rheA
ssbBSingle-strand binding protein3.5rpsF-ssbB-rpsR
mutYA/G-specific adenine glycosylase13.2mutY
radADNA repair protein0.3radA
rplURibosome and translation50S ribosomal protein L214.2rplU-rpmA
rpmA50S ribosomal protein L275.8rplU-rpmA
gatBGlutamyl-tRNA Gln amidotransferase, subunit B10.5gatCAB
rpsF30S ribosomal protein S63.4rpsF-ssbB-rpsR
0049OtherHypothetical protein5.6argR-stu0049-mutS1
0103Hypothetical protein3.6stu0103
0110Hypothetical protein poly-gamma glutamate synthesis (capsule biosynthesis)0.2stu0110-0112-0113
0161Hypothetical protein5.0stu0161
rr01Response regulatorNV0.26 ± 0.18rr01-hk01
rarDChloramphenicol sensitivity protein3.5thrB-rarD
fhsFormate-tetrahydrofolate ligase0.44cfhs
0800Methyl transferase0.3stu0800-0801
0912Hypothetical protein4.1stu0912
oxlTOxalate/formate antiporter0.2oxlT
ksgADimethyladenosine transferase4.9tatD-stu1800-ksgA
1896Predicted membrane protein4.5stu1896
  • a E, early exponential phase (2 h 30 min); L, late exponential phase (5 h 30 min); L versus E, ratio between the relative mRNA levels at 5 h 30 min and 2 h 30 min; NV, no variation; NP, not spotted on the microarray.

  • b Determined with ProFinder software (http://www.softberry.com/all.htm).

  • c Significantly differentiated genes without Bonferroni correction belonging to the putative operons identified.

  • d Underlined genes are genes with similar variations, as determined by microarray and RT-qPCR analyses.