TABLE 2.

Genes upregulated 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
qoxAAA3-600 quinol oxidase subunit II2.13.9
qoxBbAA3-600 quinol oxidase subunit I3.1
qoxCAA3-600 quinol oxidase subunit III2.6
qoxDHighly similar to quinol oxidase AA3-600 chain IV2.2
lmo0021Similar to PTS; fructose-specific IIA component2.73.53.7
lmo0022Similar to PTS; fructose-specific IIB component4.8
lmo0023Similar to PTS; fructose-specific IIC component4.6
lmo0024Similar to PTS; mannose-specific IID component5.4
lmo0039Similar to carbamate kinase2.51.9
lmo0043Similar to arginine deiminase2.93.63.2
lmo0084Similar to oxidoreductases1.8
lmo0098bSimilar to PTS; mannose specific, factor IID1.9
lmo0105bHighly similar to chitinase B5.36.9
lmo0130bSimilar to 5-nucleotidase; putative peptidoglycan-bound protein (LPXTG motif)5.29.214.7
lmo0135Similar to oligopeptide ABC transport system substrate-binding proteins1.8
lmo0153Similar to a probable high-affinity zinc ABC transporter [Zn(II)-binding lipoprotein]22.8
lmo0154Similar to high-affinity zinc ABC transporter (ATP-binding protein)2.2
lmo0155Similar to high-affinity zinc ABC transporter (membrane protein)2.3
lmo0169Similar to a glucose uptake protein2.22.13.12.8
lmo0180Similar to sugar ABC transporter; permease protein2.5
lmo0181Similar to sugar ABC transporter; sugar-binding protein2.53.3
lmo0182aSimilar to alpha-xylosidase and alpha-glucosidase2.2
lmo0183Similar to alpha-glucosidase2.3
lmo0184Similar to oligo-1,6-glucosidase1.9
prfAb,dListeriolysin-positive regulatory protein3.931.178.1
plcAb,dPhosphatidylinositol-specific phospholipase C5.1230.580.6
hlyb,dListeriolysin O precursor3.337.445.5
mplb,dZinc metalloproteinase precursor2.513.9177.5
actAb,dActin assembly-inducing protein precursor4.340106.7
plcBb,dPhospholipase C4.354165.5
lmo0206Unknown4.736.9168.8
lmo0207Hypothetical lipoprotein4.126.385.8
lmo0231Similar to arginine kinase1.8
lmo0261Similar to phospho-beta-glucosidase2.22.22.4
lmo0265Similar to succinyldiaminopimelate desuccinylase4.43.87.14.8
lmo0278Similar to sugar ABC transporter; ATP-binding protein3
lmo0298Similar to PTS beta-glucoside-specific enzyme IIC component2.53.3
lmo0299aSimilar to PTS beta-glucoside-specific enzyme IIB component2.52.55.8
lmo0300Similar to phospho-beta-glucosidase and phospho-beta-galactosidase2.52.9
lmo0342Similar to transketolase29.52.529.8
lmo0343Similar to transaldolase2.7118.15.1178.1
lmo0344Similar to dehydrogenase/reductase69.64.7113.6
lmo0345Similar to sugar-phosphate isomerase2.881.73105.7
lmo0346Similar to triosephosphate isomerase180.86.8
lmo0347Similar to dihydroxyacetone kinase2.8404.785.9
lmo0348Similar to dihydroxyacetone kinase3.1394.1120.8
lmo0358Similar to PTS; fructose-specific enzyme IIBC component2.1
lmo0384a,bSimilar to B. subtilis IolB protein4.65.4
lmo0385Similar to B. subtilis IolC protein and to fructokinase2.73
lmo0386bSimilar to B. subtilis IolD protein and to acetolactate synthase3.44.4
lmo0400Similar to fructose-specific phosphotransferase enzyme IIC2.42.5
lmo0405Similar to phosphate transport protein1.92.11.9
lmo0415Similar to endo-1,4-beta-xylanase2.0
lmo0426a,bSimilar to PTS fructose-specific enzyme IIA component2.4
lmo0427a,bSimilar to PTS fructose-specific enzyme IIB component1.83
lmo0428a,bSimilar to PTS fructose-specific enzyme IIC component2.83.43.36.4
lmo0429a,bSimilar to sugar hydrolase2.74.56.9
lmo0431Similar to acetyltransferase3.6
inlAb,dInternalin A4.32.222.216.4
inlBb,dInternalin B418.617.2
lmo0456Similar to permeases4.6
lmo0458Similar to hydantoinase2.0
lmo0498Similar to ribose 5-phosphate isomerase7.68.8
lmo0498Similar to ribose 5-phosphate isomerase7.6
lmo0499Similar to ribulose-5-phosphate 3 epimerase9
lmo0500Similar to transaldolase2.22.22.7
lmo0502a,bSimilar to putative sugar-phosphate isomerase9.819.3
lmo0503Similar to PTS fructose-specific enzyme IIA component9.622.49.3
lmo0505Similar to ribulose-5-phosphate 3-epimerase99.5
lmo0506Similar to polyol (sorbitol) dehydrogenase6.510.338.4
lmo0507a,bSimilar to PTS; galactitol-specific IIB component11.425.8
lmo0508Similar to PTS; galactitol-specific IIC component3.55.52.8
lmo0521aSimilar to 6-phospho-beta-glucosidase2.22.43.3
lmo0524Similar to putative sulfate transporter2.32.3
lmo0536bSimilar to 6-phospho-beta-glucosidase2.62.1
lmo0539Similar to tagatose-1,6-diphosphate aldolase4.23.56.95.5
lmo0546Similar to putative NAD(P)-dependent oxidoreductase1.9
lmo0554Similar to NADH-dependent butanol dehydrogenase75.310.28.5
lmo0555Similar to ditripeptide transporter222.72.9
lmo0560Similar to NADP-specific glutamate dehydrogenase3.9
lmo0610bSimilar to internalin proteins; putative peptidoglycan-bound protein (LPXTG motif)55.585.9
lmo0632bSimilar to PTS; fructose-specific IIC component2.2
lmo0640a,bSimilar to oxidoreductase2.62.72.43.9
lmo0643a,bSimilar to putative transaldolase3.45.1
lmo0650Conserved membrane protein2.52.22.22.7
lmo0669Similar to oxidoreductase3.52.87.35.0
lmo0722bSimilar to pyruvate oxidase3.53.855.1
lmo0727Similar to l-glutamine-d-fructose-6-phosphate amidotransferase2.52.6
lmo0769Similar to alpha-1,6-mannanase3
lmo0781Similar to mannose-specific PTS component IID1.92.43.32.7
lmo0782bSimilar to mannose-specific PTS component IIC2.83.35.65.0
lmo0783Similar to mannose-specific PTS component IIB3.73.56.14.8
lmo0784bSimilar to mannose-specific PTS component IIA4.335.14.6
lmo0810Similar to spermidine/putrescine-binding protein2.2
lmo0813Similar to fructokinases2.4
uhpTb,dHighly similar to hexose phosphate transport protein5.74.910.593.7
lmo0859Similar to putative sugar ABC transporter; periplasmic sugar-binding protein1.91.9
lmo0860Similar to sugar ABC transporter; permease protein2.7
lmo0861Similar to sugar ABC transporter; permease protein2.5
lmo0862Similar to oligo-1,6-glucosidase3
lmo0865Similar to phosphomannomutase33.7
lmo0875Similar to PTS; beta-glucoside enzyme IIB component2.2
lmo0876Similar to PTS; lichenan-specific enzyme IIC component1.9
lmo0877Similar to B. subtilis NagB protein (glucosamine-6-phosphate isomerase)1.9
lmo0878Similar to oxidoreductases1.9
lmo0880Similar to succinate semialdehyde dehydrogenase3.22.82.7
lmo0913bSimilar to succinate semialdehyde dehydrogenase3.735.34.7
lmo0914Similar to PTS; IIB component2.23.2
lmo0915bSimilar to PTS EIIC232.7
lmo0916Similar to PTS EIIA6.2
lmo0917Similar to beta-glucosidase4.8
lmo0956Similar to N-acetylglucosamine-6P-phosphate deacetylase (EC 3.5.1.25)2.32.73.24.2
lmo0957Similar to glucosamine-6-P isomerase (EC 5.3.1.10)2.423.9
lmo0979Similar to daunorubicin resistance ATP-binding proteins2.4
lmo1034Similar to glycerol kinase22
lmo1057Similar to l-lactate dehydrogenase22.9
lmo1097Similar to integrases3.35.1
lmo1099Similar to a protein encoded by Tn9162.5
cadACadmium resistance protein2.44.9
lmo1103Highly similar to Tn916 ORF1322.1
lmo1142Similar to Salmonella enterica PduS protein1.92.28.8
lmo1143Similar to Salmonella enterica PduT protein1.92.8
lmo1151Similar to Salmonella enterica serovar Typhimurium PduA protein9.2
lmo1152Similar to S. enterica serovar Typhimurium PduB protein14.31.910.7
lmo1154Similar to diol dehydrase (diol dehydratase) gamma subunit17.4
lmo1155Similar to diol dehydrase (diol dehydratase) gamma subunit (pddC)14.1
lmo1157Similar to diol dehydratase-reactivating factor small chain215.5
lmo1159Similar to carboxysome structural protein27.2
lmo1160Similar to Salmonella enterica PduL protein22.220.8
lmo1161Similar to ethanolamine utilization protein EutJ1.817.9
lmo1164Highly similar to Salmonella enterica PduO protein13.512.1
lmo1165Similar to ethanolamine utilization protein EutE11.3
lmo1166bSimilar to NADPH-dependent butanol dehydrogenase6.4
glpFSimilar to glycerol uptake facilitator protein13.315.3
ackA2Similar to acetate kinase3.6
lmo1180Similar to putative carboxysome structural protein2.5
lmo1205Similar to putative cobalt transport protein CbiN6.1
lmo1207Similar to cobalt transport ATP-binding protein CbiO8.7
glpDa,bSimilar to glycerol-3-phosphate dehydrogenase29.624.546.577.7
glnAHighly similar to glutamine synthetases2.31.9
lmo1349a,bSimilar to glycine dehydrogenase (decarboxylating) subunit 12.423.6
lmo1350a,bSimilar to glycine dehydrogenase (decarboxylating) subunit 2222.6
lmo1375Similar to aminotripeptidase1.82.1
lmo1389Similar to sugar ABC transporter, ATP-binding protein1.8
lmo1390Similar to ABC transporter (permease proteins)2
lmo1391Similar to sugar ABC transporter, permease protein1.9
pflBbPyruvate formate-lyase22.73.0
pflCPyruvate formate-lyase-activating enzyme22.2
lmo1421Similar to glycine betaine/carnitine/choline ABC transporter (ATP-binding protein)1.9
opuCDSimilar to betaine/carnitine/choline ABC transporter (membrane protein)1.82.62.1
opuCCSimilar to glycine betaine/carnitine/choline ABC transporter (osmoprotectant-binding protein)2.31.9
opuCBSimilar to glycine betaine/carnitine/choline ABC transporter (membrane protein)2.8
opuCASimilar to glycine betaine/carnitine/choline ABC transporter (ATP-binding protein)22.3
zurAMetal (zinc) transport protein(ABC transporter, ATP-binding protein)2.3
glyQSimilar to glycyl-tRNA synthetase alpha chain2
lmo1538a,bSimilar to glycerol kinase13.517.826.351.1
lmo1539Similar to glycerol uptake facilitator17.121.643.857.1
thrSThreonyl-tRNA synthetase1.93.0
lmo1579Similar to alanine dehydrogenase1.9
argJHighly similar to ornithine acetyltransferase and amino-acid acetyltransferases2.1
argCSimilar to N-acetylglutamate gamma-semialdehyde dehydrogenases2.7
trpAHighly similar to tryptophan synthase (alpha subunit)2.2
trpBHighly similar to tryptophan synthase (beta subunit)2
trpFPhosphoribosyl anthranilate isomerase2.6
trpCHighly similar to indol-3-glycerol phosphate synthases2.7
trpDHighly similar to anthranilate phosphoribosyltransferase2.8
trpGHighly similar to anthranilate synthase beta subunit2.3
trpEHighly similar to anthranilate synthase alpha subunit1.9
lmo1671Similar to ABC transporter and adhesion proteins1.8
inlCbInternalin C5.53.916.3
pyrEHighly similar to orotate phosphoribosyltransferases3.52.1
pyrFHighly similar to orotidine 5 -phosphate decarboxylases4.42.2
pyrDHighly similar to dihydroorotase dehydrogenase42.1
pyrDIIHighly similar to dihydroorotate dehydrogenase (electron transfer subunit)2.4
pyrABHighly similar to carbamoyl-phosphate synthetase (catalytic subunit)2.82.2
pyrAaHighly similar to carbamoyl-phosphate synthetase (glutaminase subunit)22.8
pyrCHighly similar to dihydroorotase4.5
lmo1867Similar to pyruvate phosphate dikinase4.28.67.110.0
lmo1883a,bSimilar to chitinases2.34.12.86.6
pflAa,bSimilar to pyruvate formate-lyase1.8
pnpbSimilar to purine-nucleoside phosphorylase2.22.1
drmSimilar to phosphopentomutase2.52.73.54.1
fhuGSimilar to ferrichrome ABC transporter (permease)2.1
lmo1972Similar to pentitol PTS; EIIB component21.92.3
lmo1992Similar to alpha-acetolactate decarboxylase2.5
lmo1997Similar to PTS mannose-specific enzyme IIA component2.2
lmo1998Similar to opine catabolism protein3.15.8
lmo1999bweakly similar to glucosamine-fructose-6-phosphate aminotransferase2.63.43.2
lmo2000Similar to PTS mannose-specific EIID component4.87.6
lmo2001a,bSimilar to PTS mannose-specific EIIC component3.46.25.3
lmo2002Similar to PTS mannose-specific EIIB component3.242.3
alsSSimilar to alpha-acetolactate synthase protein (AlsS)2.32.0
lmo2007Weakly similar to putative sugar-binding lipoproteins1.8
lmo2008Similar to putative ABC transporter; permease protein2.12.6
lmo2015Similar to alpha-mannosidase1.9
ileSIsoleucyl-tRNA synthetase2.4
lmo2067Similar to conjugated bile acid hydrolase6.04.84.89.0
lmo2085bPutative peptidoglycan-bound protein (LPXTG motif)3.84.76.39.0
lmo2098Similar to PTS; galactitol-specific EIA component3.33.2
lmo2108Similar to N-acetylglucosamine-6-phosphate deacetylase2.1
lmo2109Similar to hydrolase1.82.52.5
lmo2115Similar to ABC transporter (permease)3.2
lmo2121a,bSimilar to maltosephosphorylase3.6
lmo2122Similar to maltodextrose utilization protein MalA2.24
lmo2123Similar to maltodextrin ABC transport system (permease)2.74.7
lmo2124Similar to maltodextrin ABC transport system (permease)23.2
lmo2125bSimilar to maltose/maltodextrin ABC transporter (binding protein)2.74.5
lmo2134Similar to fructose-1,6-biphosphate aldolase type II2.5
lmo2135Similar to PTS; fructose-specific EIIC component2.9
lmo2136Similar to PTS; fructose-specific EIIB component3.2
lmo2143Weakly similar to mannose-6-phosphate isomerase2.3
lmo2159bSimilar to oxidoreductase2.22.63.1
lmo2175Similar to dehydrogenase3.96.3
fruAHighly similar to PTS fructose-specific EIIABC component2.22.0
lmo2341Similar to carbohydrate kinases2.23.22.6
lmo2389Similar to NADH dehydrogenase1.8
lmo2434Highly similar to glutamate decarboxylases32.54.22.7
lmo2463Similar to transport protein2.12.5
lmo2469Similar to amino acid transporter2.0
lmo2569Similar to dipeptide ABC transporter (dipeptide-binding protein)24.2
lmo2573bSimilar to zinc-binding dehydrogenase4.96.49.29.0
lmo2580Similar to ABC transporter; ATP-binding protein1.85.1
lmo2584a,bSimilar to formate dehydrogenase-associated protein7.68.4
lmo2586a,bSimilar to formate dehydrogenase alpha chain13.92839.840.5
lmo2592Similar to oxidoreductase; aldo/keto reductase family2.0
lmo2650bSimilar to hypothetical PTS enzyme IIB component2
lmo2651a,bSimilar to mannitol-specific PTS EIIA component2.1
lmo2659aSimilar to ribulose-phosphate 3-epimerase2.62.9
lmo2660aSimilar to transketolase2.2
lmo2663aSimilar to polyol dehydrogenase2.337.2
lmo2664aSimilar to sorbitol dehydrogenase3.57.24.910.9
lmo2665aSimilar to PTS; galactitol-specific EIIC component4.46.47.48.2
lmo2666a,bSimilar to PTS; galactitol-specific EIIB component5.257.68.2
lmo2667aSimilar to PTS; galactitol-specific EIIA component5.94.68.86.5
lmo2674Similar to ribose 5-phosphate epimerase2.92.63.34.5
kdpBPotassium-transporting ATPase B chain4.4
lmo2683Similar to cellobiose phosphotransferase EIIB component2.32.2
lmo2684Similar to cellobiose phosphotransferase EIIC component6.33.1
lmo2685bSimilar to cellobiose phosphotransferase EIIA component7.45.6
lmo2689Highly similar to Mg2+ transport ATPase2.43.1
lmo2695bSimilar to dihydroxyacetone kinase4.74.99.39.8
lmo2696bSimilar to hypothetical dihydroxyacetone kinase3.74.36.78.6
lmo2708Similar to PTS; cellobiose-specific EIIC18.511.111.0
lmo2733Similar to PTS; fructose-specific IIABC component3.3
lmo2735bSimilar to sucrose phosphorylase2.1
lmo2743Similar to transaldolase3.334.74.0
lmo2760Similar to ABC transporter (ATP-binding protein)3.43.1
lmo2764a,bSimilar to xylose operon regulatory protein and to glucose kinase2.21.9
lmo2772a,bSimilar to beta-glucoside-specific EIIABC1.9
bvrBa,bBeta-glucoside-specific phosphotransferase EIIABC component1.8
lmo2797bSimilar to PTS mannitol-specific EIIA3.55.6
lmo2798bSimilar to phosphatase3.16.4
lmo2799a,bSimilar to PTS mannitol-specific EIIBC3.92.711.5
lmo2800Similar to dehydrogenase2.94
lmo2848Highly similar to l-rhamnose isomerase1.9
lmo2849Similar to rhamnulokinase2.22.3
lmo2850Similar to sugar transport proteins2.1
  • a Genes upregulated in the ccpA mutant (33).

  • b Genes upregulated 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.

  • d Genes shown to be directly regulated by PrfA.