TABLE 3.

Genes downregulated in glycerol compared to glucose and cellobiose at early log phase (phase A) and late log phase (phase B) in MMc

GeneFunctionFold induction
YG-AYG-BYC-AYC-B
lmo0018Beta-glucosidase0.30.3
lmo0050Similar to sensor histidine kinase (AgrC from Staphylococcus)0.4
purASimilar to adenylosuccinate synthetase0.30.3
lmo0096Similar to PTS; mannose-specific, factor IIAB0.10.1
lmo0097Similar to PTS; mannose-specific, factor IIC0.10.1
lmo0098Similar to PTS; mannose-specific, factor IID0.10.1
lmo0135Similar to oligopeptide ABC transport system substrate-binding proteins0.5
lmo0152Similar to oligopeptide ABC transporter-binding protein0.40.6
lmo0176Similar to glucose uptake protein0.40.40.4
lmo0218Polyribonucleotide nucleotidyltransferase domain present0.50.50.4
lmo0219Fusion protein; N-terminal part similar to B. subtilis YacA protein; C-terminal part similar to hypoxanthine-guanine phosphoribosyltransferase0.50.4
cysESimilar to serine O-acetyltransferase0.40.5
lmo0269Similar to transporter0.4
lmo0271Similar to phospho-beta-glucosidase0.40.3
lmo0279Similar to anaerobic ribonucleoside-triphosphate reductase0.50.4
lmo0280Similar to anaerobic ribonucleotide reductase activator protein0.30.5
lmo0286Similar to aminotransferase0.50.4
lmo0519bSimilar to multidrug resistance protein0.5
lmo0537Similar to N-carbamyl-l-amino acid amidohydrolase0.5
lmo0560bSimilar to NADP-specific glutamate dehydrogenase0.50.5
hisDSimilar to histidinol dehydrogenases0.5
hisZHistidyl-tRNA synthetase0.50.5
lmo0611Similar to acyl-carrier protein phosphodiesterase and NAD(P)H dehydrogenase0.50.5
lmo0645Similar to amino acid transporter0.50.5
lmo0787Similar to amino acid transporter0.5
lmo0798Similar to lysine-specific permease0.3
lmo0802Weakly similar to GTP-pyrophosphokinase0.50.4
lmo0837Similar to ABC transporter (ATP-binding protein)0.5
lmo0841Similar to cation (calcium) transporting ATPase0.50.4
lmo0847Similar to glutamine ABC transporter (binding and transport protein)0.5
lmo0897Similar to transport proteins0.4
lmo0912aSimilar to transporters (formate)0.5
lmo0945Similar to C-terminal part of B. subtilis ComEC protein and to ComEA0.5
lmo0947Hypothetical transport protein0.5
lmo0960Similar to proteases0.40.40.5
lmo0981Similar to efflux transporter0.4
gbuASimilar to glycine betaine ABC transporter (ATP-binding protein)0.40.5
gbuBSimilar to glycine betaine ABC transporters (permease)0.50.40.4
gbuCa,bSimilar to glycine betaine ABC transporters (glycine betaine-binding protein)0.50.4
lmo1017Similar to phosphotransferase system glucose-specific enzyme IIA0.5
lmo1073Similar to metal binding protein (ABC transporter)0.5
pheSPhenylalany-tRNA synthetase alpha subunit0.2
pheTPhenylalanyl-tRNA synthetase beta subunit0.3
proAGamma-glutamyl phosphate reductase0.5
proBGamma-glutamyl kinase0.6
glnRSimilar to glutamine synthetase repressor0.10.1
glnASimilar to glutamine synthetases0.1
lmo1300Similar to arsenic efflux pump protein0.4
smbASimilar to uridylate kinases0.40.5
lmo1424Similar to manganese transport proteins NRAMP0.30.30.30.4
lmo1431Similar to ABC transporter (ATP-binding protein)0.5
zurMMetal (zinc) transport protein (ABC transporter, permease protein)0.5
udkSimilar to uridine kinase0.50.5
lmo1516bSimilar to ammonium transporter NrgA0.020.03
lmo1517bSimilar to nitrogen regulatory PII protein0.020.03
relASimilar to (p)ppGpp synthetase0.5
valSValyl-tRNA synthetase0.5
tyrSTyrosyl-tRNA synthetase0.50.4
aroA3-Deoxy-d-arabino-heptulosonate 7-phosphate synthase0.40.20.1
lmo1603Similar to aminopeptidase0.5
lmo1617Similar to multidrug-efflux transporter0.50.4
daaAd-Amino acid aminotransferase0.5
lmo1624Similar to putative transporters0.2
lmo1625Similar to putative transporters0.30.1
trpASimilar to tryptophan synthase (alpha subunit)0.20.1
trpBSimilar to tryptophan synthase (beta subunit)0.20.1
trpFPhosphoribosyl anthranilate isomerase0.30.2
trpCSimilar to indol-3-glycerol phosphate synthases0.30.1
trpDSimilar to anthranilate phosphoribosyltransferase0.40.2
trpGSimilar to anthranilate synthase beta subunit0.40.3
trpESimilar to anthranilate synthase alpha subunit0.50.4
lmo1634Similar to alcohol-acetaldehyde dehydrogenase0.20.30.50.1
ansBSimilar to asparaginyl-tRNA synthetases0.50.4
metKSimilar to S-methionine adenosyltransferase0.5
lmo1682Similar to transmembrane transport proteins0.4
lmo1705Similar to deoxyguanosine kinase/deoxyadenosine kinase(I) subunit0.5
lmo1719Similar to PTS lichenan-specific EIIA component0.5
lmo1720Similar to PTS lichenan-specific EIIB component0.4
lmo1730Similar to sugar ABC transporter-binding protein0.3
lmo1739Similar to amino acid (glutamine) ABC transporter (ATP-binding protein)0.6
lmo1749Similar to shikimate kinase0.30.3
purDPhosphoribosylglycinamide synthetase0.50.5
purHBifunctional phosphoribosylaminoimidazole carboxy formyl formyltransferase and inosine-monophosphate cyclohydrolase0.50.5
purNSimilar to phosphoribosylglycinamide formyltransferases0.50.4
purMPhosphoribosylaminoimidazole synthetase0.5
purFGlutamine phosphoribosylpyrophosphate amidotransferase0.4
purQPhosphoribosylformylglycinamidine synthetase I0.40.4
purQPhosphoribosylformylglycinamidine synthetase I0.40.50.4
purLSimilar to phosphoribosylformylglycinamidine synthetase II0.40.40.20.4
purCPhosphoribosylaminoimidazole succinocarboxamide synthetase0.50.50.20.4
purBAdenylosuccinate lyase0.30.50.2
purKPhosphoribosylaminoimidazole carboxylase II0.40.3
purEPhosphoribosylaminoimidazole carboxylase I0.20.40.1
lmo1778Similar to ABC transporter (ATP-binding protein)0.4
rncSSimilar to RNase III0.4
lmo1827Similar to guanylate kinases0.50.5
pyrPSimilar to uracil permease0.4
lmo1847Similar to adhesion binding proteins and lipoproteins with multiple specificity for metal cations (ABC transporter)0.40.5
lmo1848Similar metal cations ABC transporter (permease protein)0.40.40.40.5
lmo1849Similar to metal cation ABC transporter, ATP-binding proteins0.30.40.20.5
lmo1884Similar to xanthine permeases0.30.40.30.4
lmo1885Similar to xanthine phosphoribosyltransferase0.30.40.40.4
aroESimilar to 5-enolpyruvylshikimate-3-phosphate synthase0.3
tyrASimilar to prephenate dehydrogenase0.40.2
hisCSimilar to histidinol-phosphate aminotransferase and tyrosine/phenylalanine aminotransferase0.50.3
lmo1926Similar to chorismate mutase0.40.3
aroBSimilar to 3-dehydroquinate synthase0.40.2
aroFSimilar to chorismate synthase0.40.2
gpsASimilar to NAD(P)H-dependent glycerol-3-phosphate dehydrogenase0.6
lysASimilar to diaminopimelate decarboxylase0.5
fhuCSimilar to ferrichrome ABC transporter (ATP-binding protein)0.5
lmo1976Similar to oxidoreductase0.5
lmo1978Similar to glucose-6-phosphate 1-dehydrogenase0.40.50.40.3
ilvDSimilar to dihydroxy acid dehydratase0.40.40.50.3
ilvBSimilar to acetolactate synthase (acetohydroxy acid synthase) (large subunit)0.5
leuASimilar to 2-isopropylmalate synthase0.5
leuBbSimilar to 3-isopropylmalate dehydrogenase0.5
lmo2075Similar to glycoprotein endopeptidase0.5
lmo2110Similar to mannnose-6 phosphate isomerase0.30.5
lmo2114Similar to ABC transporter (ATP-binding protein)0.3
lmo2152Similar to thioredoxin0.5
lmo2153Similar to flavodoxin0.5
lmo2192bSimilar to oligopeptide ABC transporter (ATP-binding protein)0.5
lmo2193bSimilar to oligopeptide ABC transporter (ATP-binding protein)0.5
lmo2194bSimilar to oligopeptide ABC transporter (permease)0.40.5
lmo2195bSimilar to oligopeptide ABC transporter (permease)0.50.5
lmo2196Similar to pheromone ABC transporter (binding protein)0.40.3
lmo2238Similar to transport system permease protein0.50.3
arpJSimilar to amino acid ABC transporter, permease protein0.50.3
lmo2346Similar to amino acid ABC transporter, ATP-binding protein0.5
lmo2348Similar to amino acid ABC transporter (permease)0.40.5
lmo2349Similar to amino acid ABC transporter (binding protein)0.5
lmo2355Similar to multidrug resistance protein0.50.5
lmo2371Similar to putative ABC transporter transmembrane subunit0.5
lmo2372Similar to ABC transporter ATP binding proteins0.5
lmo2374Similar to aspartate kinase0.50.5
lmo2377Similar to multidrug resistance efflux pump0.50.6
lmo2421Similar to two-component sensor histidine kinase0.5
lmo2430Similar to B. subtilis ferrichrome ABC transporter (permease) FhuG0.50.5
lmo2431Similar to B. subtilis ferrichrome ABC transporter fhuD precursor (ferrichrome-binding protein)0.5
enoSimilar to enolase0.4
pgmSimilar to phosphoglycerate mutase0.40.3
tpiSimilar to triose phosphate isomerase0.50.3
pgkSimilar to phosphoglycerate kinase0.30.3
gapSimilar to glyceraldehyde-3-phosphate dehydrogenase0.50.40.3
atpHSimilar to H+-transporting ATP synthase chain delta0.4
atpFSimilar to H+-transporting ATP synthase chain b0.5
atpESimilar to H+-transporting ATP synthase chain c0.5
atpBSimilar to H+-transporting ATP synthase chain a0.5
atpISimilar to ATP synthase subunit i0.5
uppSimilar to uracil phosphoribosyltransferase0.5
glyASimilar to glycine hydroxymethyltransferase0.5
homSimilar to homoserine dehydrogenase0.50.50.40.4
fbaASimilar to fructose-1,6-bisphosphate aldolase0.50.4
lmo2601Similar to ABC transporter (ATP-binding protein)0.5
lmo2684Similar to cellobiose phosphotransferase EIIC component0.6
lmo2720Similar to acetate-coenzyme A ligase0.50.40.4
serSSeryl-tRNA synthetase0.50.2
guaBSimilar to inosine-monophosphate dehydrogenase0.5
lmo2769Similar to ABC transporter, ATP-binding protein0.50.5
lmo2824Similar to d-3-phosphoglycerate dehydrogenase0.6
serCSimilar to phosphoserine aminotransferase0.4
  • a Gene downregulated in the ccpA mutant (33).

  • b Gene downregulated in the hprK mutant (33).

  • c Values indicate regulation, and no value indicates no regulation of the gene under the conditions mentioned. The genes discussed in this study are indicated in boldface type. The complete list of differentially regulated genes is available in Table S2 in the supplemental material. Y, glycerol; G, glucose; C, cellobiose; A, phase A; B, phase B.