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. 2008 May 23;190(15):5412–5430. doi: 10.1128/JB.00259-08

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

Gene Function Fold induction
YG-A YG-B YC-A YC-B
qoxA AA3-600 quinol oxidase subunit II 2.1 3.9
qoxBb AA3-600 quinol oxidase subunit I 3.1
qoxC AA3-600 quinol oxidase subunit III 2.6
qoxD Highly similar to quinol oxidase AA3-600 chain IV 2.2
lmo0021 Similar to PTS; fructose-specific IIA component 2.7 3.5 3.7
lmo0022 Similar to PTS; fructose-specific IIB component 4.8
lmo0023 Similar to PTS; fructose-specific IIC component 4.6
lmo0024 Similar to PTS; mannose-specific IID component 5.4
lmo0039 Similar to carbamate kinase 2.5 1.9
lmo0043 Similar to arginine deiminase 2.9 3.6 3.2
lmo0084 Similar to oxidoreductases 1.8
lmo0098b Similar to PTS; mannose specific, factor IID 1.9
lmo0105b Highly similar to chitinase B 5.3 6.9
lmo0130b Similar to 5-nucleotidase; putative peptidoglycan-bound protein (LPXTG motif) 5.2 9.2 14.7
lmo0135 Similar to oligopeptide ABC transport system substrate-binding proteins 1.8
lmo0153 Similar to a probable high-affinity zinc ABC transporter [Zn(II)-binding lipoprotein] 2 2.8
lmo0154 Similar to high-affinity zinc ABC transporter (ATP-binding protein) 2.2
lmo0155 Similar to high-affinity zinc ABC transporter (membrane protein) 2.3
lmo0169 Similar to a glucose uptake protein 2.2 2.1 3.1 2.8
lmo0180 Similar to sugar ABC transporter; permease protein 2.5
lmo0181 Similar to sugar ABC transporter; sugar-binding protein 2.5 3.3
lmo0182a Similar to alpha-xylosidase and alpha-glucosidase 2.2
lmo0183 Similar to alpha-glucosidase 2.3
lmo0184 Similar to oligo-1,6-glucosidase 1.9
prfAb,d Listeriolysin-positive regulatory protein 3.9 31.1 78.1
plcAb,d Phosphatidylinositol-specific phospholipase C 5.1 2 30.5 80.6
hlyb,d Listeriolysin O precursor 3.3 37.4 45.5
mplb,d Zinc metalloproteinase precursor 2.5 13.9 177.5
actAb,d Actin assembly-inducing protein precursor 4.3 40 106.7
plcBb,d Phospholipase C 4.3 54 165.5
lmo0206 Unknown 4.7 36.9 168.8
lmo0207 Hypothetical lipoprotein 4.1 26.3 85.8
lmo0231 Similar to arginine kinase 1.8
lmo0261 Similar to phospho-beta-glucosidase 2.2 2.2 2.4
lmo0265 Similar to succinyldiaminopimelate desuccinylase 4.4 3.8 7.1 4.8
lmo0278 Similar to sugar ABC transporter; ATP-binding protein 3
lmo0298 Similar to PTS beta-glucoside-specific enzyme IIC component 2.5 3.3
lmo0299a Similar to PTS beta-glucoside-specific enzyme IIB component 2.5 2.5 5.8
lmo0300 Similar to phospho-beta-glucosidase and phospho-beta-galactosidase 2.5 2.9
lmo0342 Similar to transketolase 29.5 2.5 29.8
lmo0343 Similar to transaldolase 2.7 118.1 5.1 178.1
lmo0344 Similar to dehydrogenase/reductase 69.6 4.7 113.6
lmo0345 Similar to sugar-phosphate isomerase 2.8 81.7 3 105.7
lmo0346 Similar to triosephosphate isomerase 180.8 6.8
lmo0347 Similar to dihydroxyacetone kinase 2.8 40 4.7 85.9
lmo0348 Similar to dihydroxyacetone kinase 3.1 39 4.1 120.8
lmo0358 Similar to PTS; fructose-specific enzyme IIBC component 2.1
lmo0384a,b Similar to B. subtilis IolB protein 4.6 5.4
lmo0385 Similar to B. subtilis IolC protein and to fructokinase 2.7 3
lmo0386b Similar to B. subtilis IolD protein and to acetolactate synthase 3.4 4.4
lmo0400 Similar to fructose-specific phosphotransferase enzyme IIC 2.4 2.5
lmo0405 Similar to phosphate transport protein 1.9 2.1 1.9
lmo0415 Similar to endo-1,4-beta-xylanase 2.0
lmo0426a,b Similar to PTS fructose-specific enzyme IIA component 2.4
lmo0427a,b Similar to PTS fructose-specific enzyme IIB component 1.8 3
lmo0428a,b Similar to PTS fructose-specific enzyme IIC component 2.8 3.4 3.3 6.4
lmo0429a,b Similar to sugar hydrolase 2.7 4.5 6.9
lmo0431 Similar to acetyltransferase 3.6
inlAb,d Internalin A 4.3 2.2 22.2 16.4
inlBb,d Internalin B 4 18.6 17.2
lmo0456 Similar to permeases 4.6
lmo0458 Similar to hydantoinase 2.0
lmo0498 Similar to ribose 5-phosphate isomerase 7.6 8.8
lmo0498 Similar to ribose 5-phosphate isomerase 7.6
lmo0499 Similar to ribulose-5-phosphate 3 epimerase 9
lmo0500 Similar to transaldolase 2.2 2.2 2.7
lmo0502a,b Similar to putative sugar-phosphate isomerase 9.8 19.3
lmo0503 Similar to PTS fructose-specific enzyme IIA component 9.6 22.4 9.3
lmo0505 Similar to ribulose-5-phosphate 3-epimerase 9 9.5
lmo0506 Similar to polyol (sorbitol) dehydrogenase 6.5 10.3 38.4
lmo0507a,b Similar to PTS; galactitol-specific IIB component 11.4 25.8
lmo0508 Similar to PTS; galactitol-specific IIC component 3.5 5.5 2.8
lmo0521a Similar to 6-phospho-beta-glucosidase 2.2 2.4 3.3
lmo0524 Similar to putative sulfate transporter 2.3 2.3
lmo0536b Similar to 6-phospho-beta-glucosidase 2.6 2.1
lmo0539 Similar to tagatose-1,6-diphosphate aldolase 4.2 3.5 6.9 5.5
lmo0546 Similar to putative NAD(P)-dependent oxidoreductase 1.9
lmo0554 Similar to NADH-dependent butanol dehydrogenase 7 5.3 10.2 8.5
lmo0555 Similar to ditripeptide transporter 2 2 2.7 2.9
lmo0560 Similar to NADP-specific glutamate dehydrogenase 3.9
lmo0610b Similar to internalin proteins; putative peptidoglycan-bound protein (LPXTG motif) 5 5.5 8 5.9
lmo0632b Similar to PTS; fructose-specific IIC component 2.2
lmo0640a,b Similar to oxidoreductase 2.6 2.7 2.4 3.9
lmo0643a,b Similar to putative transaldolase 3.4 5.1
lmo0650 Conserved membrane protein 2.5 2.2 2.2 2.7
lmo0669 Similar to oxidoreductase 3.5 2.8 7.3 5.0
lmo0722b Similar to pyruvate oxidase 3.5 3.8 5 5.1
lmo0727 Similar to l-glutamine-d-fructose-6-phosphate amidotransferase 2.5 2.6
lmo0769 Similar to alpha-1,6-mannanase 3
lmo0781 Similar to mannose-specific PTS component IID 1.9 2.4 3.3 2.7
lmo0782b Similar to mannose-specific PTS component IIC 2.8 3.3 5.6 5.0
lmo0783 Similar to mannose-specific PTS component IIB 3.7 3.5 6.1 4.8
lmo0784b Similar to mannose-specific PTS component IIA 4.3 3 5.1 4.6
lmo0810 Similar to spermidine/putrescine-binding protein 2.2
lmo0813 Similar to fructokinases 2.4
uhpTb,d Highly similar to hexose phosphate transport protein 5.7 4.9 10.5 93.7
lmo0859 Similar to putative sugar ABC transporter; periplasmic sugar-binding protein 1.9 1.9
lmo0860 Similar to sugar ABC transporter; permease protein 2.7
lmo0861 Similar to sugar ABC transporter; permease protein 2.5
lmo0862 Similar to oligo-1,6-glucosidase 3
lmo0865 Similar to phosphomannomutase 3 3.7
lmo0875 Similar to PTS; beta-glucoside enzyme IIB component 2.2
lmo0876 Similar to PTS; lichenan-specific enzyme IIC component 1.9
lmo0877 Similar to B. subtilis NagB protein (glucosamine-6-phosphate isomerase) 1.9
lmo0878 Similar to oxidoreductases 1.9
lmo0880 Similar to succinate semialdehyde dehydrogenase 3.2 2.8 2.7
lmo0913b Similar to succinate semialdehyde dehydrogenase 3.7 3 5.3 4.7
lmo0914 Similar to PTS; IIB component 2.2 3.2
lmo0915b Similar to PTS EIIC 2 3 2.7
lmo0916 Similar to PTS EIIA 6.2
lmo0917 Similar to beta-glucosidase 4.8
lmo0956 Similar to N-acetylglucosamine-6P-phosphate deacetylase (EC 3.5.1.25) 2.3 2.7 3.2 4.2
lmo0957 Similar to glucosamine-6-P isomerase (EC 5.3.1.10) 2.4 2 3.9
lmo0979 Similar to daunorubicin resistance ATP-binding proteins 2.4
lmo1034 Similar to glycerol kinase 2 2
lmo1057 Similar to l-lactate dehydrogenase 2 2.9
lmo1097 Similar to integrases 3.3 5.1
lmo1099 Similar to a protein encoded by Tn916 2.5
cadA Cadmium resistance protein 2.4 4.9
lmo1103 Highly similar to Tn916 ORF13 2 2.1
lmo1142 Similar to Salmonella enterica PduS protein 1.9 2.2 8.8
lmo1143 Similar to Salmonella enterica PduT protein 1.9 2.8
lmo1151 Similar to Salmonella enterica serovar Typhimurium PduA protein 9.2
lmo1152 Similar to S. enterica serovar Typhimurium PduB protein 14.3 1.9 10.7
lmo1154 Similar to diol dehydrase (diol dehydratase) gamma subunit 17.4
lmo1155 Similar to diol dehydrase (diol dehydratase) gamma subunit (pddC) 14.1
lmo1157 Similar to diol dehydratase-reactivating factor small chain 2 15.5
lmo1159 Similar to carboxysome structural protein 27.2
lmo1160 Similar to Salmonella enterica PduL protein 22.2 20.8
lmo1161 Similar to ethanolamine utilization protein EutJ 1.8 17.9
lmo1164 Highly similar to Salmonella enterica PduO protein 13.5 12.1
lmo1165 Similar to ethanolamine utilization protein EutE 11.3
lmo1166b Similar to NADPH-dependent butanol dehydrogenase 6.4
glpF Similar to glycerol uptake facilitator protein 13.3 15.3
ackA2 Similar to acetate kinase 3.6
lmo1180 Similar to putative carboxysome structural protein 2.5
lmo1205 Similar to putative cobalt transport protein CbiN 6.1
lmo1207 Similar to cobalt transport ATP-binding protein CbiO 8.7
glpDa,b Similar to glycerol-3-phosphate dehydrogenase 29.6 24.5 46.5 77.7
glnA Highly similar to glutamine synthetases 2.3 1.9
lmo1349a,b Similar to glycine dehydrogenase (decarboxylating) subunit 1 2.4 2 3.6
lmo1350a,b Similar to glycine dehydrogenase (decarboxylating) subunit 2 2 2 2.6
lmo1375 Similar to aminotripeptidase 1.8 2.1
lmo1389 Similar to sugar ABC transporter, ATP-binding protein 1.8
lmo1390 Similar to ABC transporter (permease proteins) 2
lmo1391 Similar to sugar ABC transporter, permease protein 1.9
pflBb Pyruvate formate-lyase 2 2.7 3.0
pflC Pyruvate formate-lyase-activating enzyme 2 2.2
lmo1421 Similar to glycine betaine/carnitine/choline ABC transporter (ATP-binding protein) 1.9
opuCD Similar to betaine/carnitine/choline ABC transporter (membrane protein) 1.8 2.6 2.1
opuCC Similar to glycine betaine/carnitine/choline ABC transporter (osmoprotectant-binding protein) 2.3 1.9
opuCB Similar to glycine betaine/carnitine/choline ABC transporter (membrane protein) 2.8
opuCA Similar to glycine betaine/carnitine/choline ABC transporter (ATP-binding protein) 2 2.3
zurA Metal (zinc) transport protein(ABC transporter, ATP-binding protein) 2.3
glyQ Similar to glycyl-tRNA synthetase alpha chain 2
lmo1538a,b Similar to glycerol kinase 13.5 17.8 26.3 51.1
lmo1539 Similar to glycerol uptake facilitator 17.1 21.6 43.8 57.1
thrS Threonyl-tRNA synthetase 1.9 3.0
lmo1579 Similar to alanine dehydrogenase 1.9
argJ Highly similar to ornithine acetyltransferase and amino-acid acetyltransferases 2.1
argC Similar to N-acetylglutamate gamma-semialdehyde dehydrogenases 2.7
trpA Highly similar to tryptophan synthase (alpha subunit) 2.2
trpB Highly similar to tryptophan synthase (beta subunit) 2
trpF Phosphoribosyl anthranilate isomerase 2.6
trpC Highly similar to indol-3-glycerol phosphate synthases 2.7
trpD Highly similar to anthranilate phosphoribosyltransferase 2.8
trpG Highly similar to anthranilate synthase beta subunit 2.3
trpE Highly similar to anthranilate synthase alpha subunit 1.9
lmo1671 Similar to ABC transporter and adhesion proteins 1.8
inlCb Internalin C 5.5 3.9 16.3
pyrE Highly similar to orotate phosphoribosyltransferases 3.5 2.1
pyrF Highly similar to orotidine 5 -phosphate decarboxylases 4.4 2.2
pyrD Highly similar to dihydroorotase dehydrogenase 4 2.1
pyrDII Highly similar to dihydroorotate dehydrogenase (electron transfer subunit) 2.4
pyrAB Highly similar to carbamoyl-phosphate synthetase (catalytic subunit) 2.8 2.2
pyrAa Highly similar to carbamoyl-phosphate synthetase (glutaminase subunit) 2 2.8
pyrC Highly similar to dihydroorotase 4.5
lmo1867 Similar to pyruvate phosphate dikinase 4.2 8.6 7.1 10.0
lmo1883a,b Similar to chitinases 2.3 4.1 2.8 6.6
pflAa,b Similar to pyruvate formate-lyase 1.8
pnpb Similar to purine-nucleoside phosphorylase 2.2 2.1
drm Similar to phosphopentomutase 2.5 2.7 3.5 4.1
fhuG Similar to ferrichrome ABC transporter (permease) 2.1
lmo1972 Similar to pentitol PTS; EIIB component 2 1.9 2.3
lmo1992 Similar to alpha-acetolactate decarboxylase 2.5
lmo1997 Similar to PTS mannose-specific enzyme IIA component 2.2
lmo1998 Similar to opine catabolism protein 3.1 5.8
lmo1999b weakly similar to glucosamine-fructose-6-phosphate aminotransferase 2.6 3.4 3.2
lmo2000 Similar to PTS mannose-specific EIID component 4.8 7.6
lmo2001a,b Similar to PTS mannose-specific EIIC component 3.4 6.2 5.3
lmo2002 Similar to PTS mannose-specific EIIB component 3.2 4 2.3
alsS Similar to alpha-acetolactate synthase protein (AlsS) 2.3 2.0
lmo2007 Weakly similar to putative sugar-binding lipoproteins 1.8
lmo2008 Similar to putative ABC transporter; permease protein 2.1 2.6
lmo2015 Similar to alpha-mannosidase 1.9
ileS Isoleucyl-tRNA synthetase 2.4
lmo2067 Similar to conjugated bile acid hydrolase 6.0 4.8 4.8 9.0
lmo2085b Putative peptidoglycan-bound protein (LPXTG motif) 3.8 4.7 6.3 9.0
lmo2098 Similar to PTS; galactitol-specific EIA component 3.3 3.2
lmo2108 Similar to N-acetylglucosamine-6-phosphate deacetylase 2.1
lmo2109 Similar to hydrolase 1.8 2.5 2.5
lmo2115 Similar to ABC transporter (permease) 3.2
lmo2121a,b Similar to maltosephosphorylase 3.6
lmo2122 Similar to maltodextrose utilization protein MalA 2.2 4
lmo2123 Similar to maltodextrin ABC transport system (permease) 2.7 4.7
lmo2124 Similar to maltodextrin ABC transport system (permease) 2 3.2
lmo2125b Similar to maltose/maltodextrin ABC transporter (binding protein) 2.7 4.5
lmo2134 Similar to fructose-1,6-biphosphate aldolase type II 2.5
lmo2135 Similar to PTS; fructose-specific EIIC component 2.9
lmo2136 Similar to PTS; fructose-specific EIIB component 3.2
lmo2143 Weakly similar to mannose-6-phosphate isomerase 2.3
lmo2159b Similar to oxidoreductase 2.2 2.6 3.1
lmo2175 Similar to dehydrogenase 3.9 6.3
fruA Highly similar to PTS fructose-specific EIIABC component 2.2 2.0
lmo2341 Similar to carbohydrate kinases 2.2 3.2 2.6
lmo2389 Similar to NADH dehydrogenase 1.8
lmo2434 Highly similar to glutamate decarboxylases 3 2.5 4.2 2.7
lmo2463 Similar to transport protein 2.1 2.5
lmo2469 Similar to amino acid transporter 2.0
lmo2569 Similar to dipeptide ABC transporter (dipeptide-binding protein) 2 4.2
lmo2573b Similar to zinc-binding dehydrogenase 4.9 6.4 9.2 9.0
lmo2580 Similar to ABC transporter; ATP-binding protein 1.8 5.1
lmo2584a,b Similar to formate dehydrogenase-associated protein 7.6 8.4
lmo2586a,b Similar to formate dehydrogenase alpha chain 13.9 28 39.8 40.5
lmo2592 Similar to oxidoreductase; aldo/keto reductase family 2.0
lmo2650b Similar to hypothetical PTS enzyme IIB component 2
lmo2651a,b Similar to mannitol-specific PTS EIIA component 2.1
lmo2659a Similar to ribulose-phosphate 3-epimerase 2.6 2.9
lmo2660a Similar to transketolase 2.2
lmo2663a Similar to polyol dehydrogenase 2.3 3 7.2
lmo2664a Similar to sorbitol dehydrogenase 3.5 7.2 4.9 10.9
lmo2665a Similar to PTS; galactitol-specific EIIC component 4.4 6.4 7.4 8.2
lmo2666a,b Similar to PTS; galactitol-specific EIIB component 5.2 5 7.6 8.2
lmo2667a Similar to PTS; galactitol-specific EIIA component 5.9 4.6 8.8 6.5
lmo2674 Similar to ribose 5-phosphate epimerase 2.9 2.6 3.3 4.5
kdpB Potassium-transporting ATPase B chain 4.4
lmo2683 Similar to cellobiose phosphotransferase EIIB component 2.3 2.2
lmo2684 Similar to cellobiose phosphotransferase EIIC component 6.3 3.1
lmo2685b Similar to cellobiose phosphotransferase EIIA component 7.4 5.6
lmo2689 Highly similar to Mg2+ transport ATPase 2.4 3.1
lmo2695b Similar to dihydroxyacetone kinase 4.7 4.9 9.3 9.8
lmo2696b Similar to hypothetical dihydroxyacetone kinase 3.7 4.3 6.7 8.6
lmo2708 Similar to PTS; cellobiose-specific EIIC 18.5 11.1 11.0
lmo2733 Similar to PTS; fructose-specific IIABC component 3.3
lmo2735b Similar to sucrose phosphorylase 2.1
lmo2743 Similar to transaldolase 3.3 3 4.7 4.0
lmo2760 Similar to ABC transporter (ATP-binding protein) 3.4 3.1
lmo2764a,b Similar to xylose operon regulatory protein and to glucose kinase 2.2 1.9
lmo2772a,b Similar to beta-glucoside-specific EIIABC 1.9
bvrBa,b Beta-glucoside-specific phosphotransferase EIIABC component 1.8
lmo2797b Similar to PTS mannitol-specific EIIA 3.5 5.6
lmo2798b Similar to phosphatase 3.1 6.4
lmo2799a,b Similar to PTS mannitol-specific EIIBC 3.9 2.7 11.5
lmo2800 Similar to dehydrogenase 2.9 4
lmo2848 Highly similar to l-rhamnose isomerase 1.9
lmo2849 Similar to rhamnulokinase 2.2 2.3
lmo2850 Similar to sugar transport proteins 2.1
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.