Table 1.
Genes differentially trnascribed on plates or in liquid
| Gene Name | Gene Product | Locus tag | DGE (LFC)a | FDR (q value) a |
|---|---|---|---|---|
| Genes transcribed at higher levels on plates than liquid | ||||
| fus | Elongation factor G | CPE0079 | 2.010 | 0.0276 |
| mdh | Alcohol dehydrogenase | CPE0085 | 5.323 | 0.0405 |
| iolB | Myo-inositol catabolism protein | CPE0088 | 5.361 | 0.0276 |
| iolD | Myo-inositol catabolism protein | CPE0089 | 5.840 | 0.0276 |
| mviM | Probable dehydrogenase | CPE0090 | 6.458 | 0.0405 |
| iolE | Myo-inositol catabolism protein | CPE0091 | 6.367 | 0.0405 |
| Na+/myo-inositol cotransporter | CPE0092 | 6.517 | 0.0405 | |
| mviM | Probable dehydrogenase | CPE0093 | 6.825 | 0.0405 |
| caiD | Crotonase | CPE0095 | 6.801 | 0.0405 |
| Propionate CoA-transferase | CPE0096 | 6.666 | 0.0405 | |
| acdS | Acyl-CoA dehydrogenase | CPE0097 | 6.615 | 0.0276 |
| gldA | Glycerol dehydrogenase | CPE0099 | 3.575 | 0.0405 |
| ldh | L-lactate dehydrogenase | CPE0103 | 2.347 | 0.0276 |
| Hypothetical protein | CPE0105 | 2.200 | 0.0276 | |
| Hypothetical protein | CPE0113 | 4.346 | 0.0405 | |
| Probable transposase | CPE0139 | 2.209 | 0.0405 | |
| rbsK | 2-keto-3-deoxygluconate kinase | CPE0146 | 3.584 | 0.0405 |
| bglR | Beta-glucuronidase | CPE0147 | 2.973 | 0.0276 |
| fabG | Probable oxidoreductase | CPE0149 | 4.098 | 0.0276 |
| eda | KDPG/KHG aldolase | CPE0150 | 4.529 | 0.0276 |
| uxuA | D-mannonate dehydrolase | CPE0151 | 4.598 | 0.0276 |
| uxaC | Glucuronate isomerase | CPE0152 | 4.107 | 0.0276 |
| uidB | Glucuronide permease | CPE0153 | 3.929 | 0.0508 |
| bglX | Probable beta-hexosamidase A | CPE0154 | 3.756 | 0.0276 |
| potE | Membrane-spanning transporter protein | CPE0166 | 5.109 | 0.0276 |
| pbg | Beta-galactosidase | CPE0167 | 6.142 | 0.0276 |
| arcA | Arginine deiminase | CPE0168 | 8.558 | 0.0276 |
| arcB | Ornithine carbamoyl transferase | CPE0169 | 9.532 | 0.0276 |
| arcD | Arginine ornithine antiporter | CPE0170 | 9.285 | 0.0405 |
| arcC | Carbamate kinase | CPE0171 | 10.053 | 0.0276 |
| argR | Arginine repressor | CPE0172 | 9.292 | 0.0276 |
| ackA | Acetate kinase | CPE0217 | 2.473 | 0.0276 |
| galE | UDP-glucose 4-epimerase | CPE0286 | 2.507 | 0.0276 |
| lldP | Probable lactate permease | CPE0310 | 4.960 | 0.0405 |
| etfB | Electron transfer flavoprotein beta-subunit | CPE0311 | 5.305 | 0.0405 |
| etfA | Electron transfer flavoprotein alpha-subunit | CPE0312 | 5.131 | 0.0405 |
| glcD | Probable glycolate oxidase subunit | CPE0313 | 5.530 | 0.0405 |
| fucK | Rhamnulokinase | CPE0317 | 4.832 | 0.0405 |
| fucI | L-fucose isomerase | CPE0318 | 5.490 | 0.0405 |
| fucA | L-fuculose-phosphate aldolase | CPE0319 | 5.211 | 0.0405 |
| manX | Phosphotransferase system, mannose/fructose-specific component IIA | CPE0320 | 5.914 | 0.0405 |
| manY | Probable PTS system | CPE0322 | 5.990 | 0.0405 |
| manZ | Probable PTS system | CPE0323 | 5.472 | 0.0276 |
| Probable glycosyl hydrolase | CPE0324 | 4.220 | 0.0405 | |
| Hypothetical protein | CPE0325 | 4.582 | 0.0276 | |
| lacA | Galactose-6-phosphate isomerase | CPE0326 | 3.756 | 0.0276 |
| lacB | Galactose-6-phosphate isomerase | CPE0327 | 4.059 | 0.0405 |
| Hypothetical protein | CPE0329 | 3.447 | 0.0405 | |
| mgtA | Probable cation-transporting ATPase | CPE0333 | 2.606 | 0.0276 |
| ugpB | ABC-type sugar transport system, periplasmic component | CPE0371 | 3.351 | 0.0405 |
| ugpA | Probable ABC transporter | CPE0372 | 3.083 | 0.0405 |
| ugpE | Probable ABC transporter | CPE0373 | 3.126 | 0.0405 |
| aga | Alpha-galactosidase | CPE0374 | 3.251 | 0.0276 |
| skn1 | Endo-beta-galactosidase C | CPE0375 | 3.511 | 0.0276 |
| arcD | Probable amino acid permease | CPE0389 | 3.325 | 0.0276 |
| dchS | Histidine decarboxylase | CPE0390 | 3.404 | 0.0276 |
| Conserved hypothetical protein, six-hairpin glycosidase | CPE0426 | 3.005 | 0.0276 | |
| dedA | Alkaline phosphatase-like protein | CPE0455 | 4.214 | 0.0405 |
| Conserved hypothetical protein | CPE0456 | 5.954 | 0.0405 | |
| nanJ | Exo-alpha-sialidase | CPE0553 | 3.651 | 0.0405 |
| Hypothetical protein | CPE0554 | 4.438 | 0.0405 | |
| Hypothetical protein, in sigV operon | CPE0560 | 3.806 | 0.0405 | |
| ribB | Riboflavin biosynthesis protein | CPE0566 | 4.731 | 0.0405 |
| pflA | Pyruvate-formate lyase-activating enzyme | CPE0660 | 2.014 | 0.0276 |
| Hypothetical protein | CPE0669 | 2.475 | 0.0276 | |
| nanI | Exo-alpha-sialidase | CPE0725 | 2.373 | 0.0276 |
| lipB | Probable lipase | CPE0742 | 2.368 | 0.0276 |
| cstA | Probable carbon starvation protein (peptide utilization) | CPE0743 | 2.902 | 0.0276 |
| fepG | Probable iron (III) dicitrate ABC transporter | CPE0794 | 2.994 | 0.0405 |
| Conserved hypothetical protein | CPE0806 | 2.526 | 0.0276 | |
| Hypothetical protein | CPE0808 | 2.776 | 0.0276 | |
| Endo-beta-N-acetylglucosaminidase | CPE0818 | 4.763 | 0.0405 | |
| rubY | Rubrerythrin | CPE0855 | 5.144 | 0.0276 |
| ams1 | Alpha-mannosidase | CPE0856 | 2.716 | 0.0276 |
| gntT | Probable gluconate permease | CPE0860 | 2.095 | 0.0498 |
| Hypothetical protein | CPE0863 | 2.281 | 0.0276 | |
| Hypothetical protein | CPE0876 | 2.380 | 0.0276 | |
| pduL | Probable propanediol utilization protein | CPE0905 | 4.429 | 0.0276 |
| nrdD | Probable anaerobic ribonucleotide reductase | CPE0917 | 3.741 | 0.0276 |
| Hypothetical protein | CPE0918 | 3.713 | 0.0405 | |
| Hypothetical protein | CPE0919 | 2.303 | 0.0405 | |
| pduC | Coenzyme B12-dependent glycerol dehydrogenase large subunit | CPE0929 | 4.916 | 0.0405 |
| Coenzyme B12-dependent glycerol dehydrogenase medium subunit | CPE0930 | 5.177 | 0.0276 | |
| pduE | Coenzyme B12-dependent glycerol dehydrogenase small subunit | CPE0931 | 4.927 | 0.0276 |
| Probable glycerol dehydratase large subunit | CPE0932 | 5.155 | 0.0276 | |
| Conserved hypothetical protein | CPE0934 | 4.864 | 0.0405 | |
| Hypothetical protein | CPE0982 | 3.345 | 0.0276 | |
| sdhB | L-serine dehydratase beta subunit | CPE0988 | 2.614 | 0.0405 |
| sdhA | L-serine dehydratase alpha subunit | CPE0989 | 2.606 | 0.0276 |
| tdcF | Probable translation initiation inhibitor | CPE1012 | 2.954 | 0.0405 |
| thd | Threonine dehydratase | CPE1165 | 2.659 | 0.0276 |
| gltP | Probable glutamate/ aspartate transporter | CPE1167 | 4.116 | 0.0276 |
| pfk | 6-phosphofructokinase | CPE1185 | 2.492 | 0.0276 |
| ugpB | ABC-type sugar transport system, periplasmic component | CPE1257 | 5.358 | 0.0405 |
| eno | Enolase | CPE1299 | 2.171 | 0.0405 |
| galM | Aldose 1-epimerase | CPE1344 | 3.795 | 0.0276 |
| galK | Galactokinase | CPE1345 | 3.935 | 0.0405 |
| galT | Galactose-1-phosphate-uridyl transferase | CPE1346 | 5.420 | 0.0405 |
| ams1 | Alpha-mannosidase | CPE1415 | 2.732 | 0.0276 |
| clpB | ATPase with chaperonin activity | CPE1428 | 2.641 | 0.0276 |
| Uncharacterized membrane protein, peptidase | CPE1452 | 2.064 | 0.0276 | |
| Hypothetical protein | CPE1592 | 2.340 | 0.0276 | |
| purR | Probable transcriptional regulator, LacI/PurR family | CPE1626 | 3.087 | 0.0276 |
| rbsB | Probable ribose ABC transporter | CPE1627 | 3.103 | 0.0276 |
| rbsC | Probable ribose ABC transporter | CPE1629 | 2.619 | 0.0405 |
| rbsA | Probable ribose ABC transporter | CPE1630 | 2.403 | 0.0276 |
| trmU | Probable tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase | CPE1783 | 2.530 | 0.0276 |
| nifU | Probable nitrogen fixation protein | CPE1784 | 2.309 | 0.0276 |
| dacF | Serine-type D-Ala-D-Ala carboxypeptidase | CPE1806 | 2.596 | 0.0276 |
| deoA | Pyrimidine-nucleoside phosphorylase | CPE1807 | 2.672 | 0.0276 |
| Alpha-L-fucosidase | CPE1876 | 3.336 | 0.0405 | |
| hipB | Predicted transcriptional regulator | CPE1967 | 3.060 | 0.0405 |
| potB | Probable spermidine/putrescine ABC transporter | CPE1969 | 2.143 | 0.0405 |
| pldB | Lysophospholipase | CPE1989 | 2.345 | 0.0276 |
| podK | Pyruvate phosphate dikinase | CPE2011 | 2.691 | 0.0276 |
| potE | Probable glutamate gamma-aminobutyrate antiporter | CPE2060 | 2.994 | 0.0405 |
| Alpha-glucosidase | CPE2076 | 2.114 | 0.0405 | |
| nagC | Probable transcriptional regulator | CPE2077 | 2.213 | 0.0405 |
| ugpB | ABC-type sugar transport system, periplasmic component | CPE2078 | 3.148 | 0.0405 |
| ugpE | Probable ABC transporter | CPE2081 | 3.132 | 0.0405 |
| lplB | Probable ABC transporter | CPE2082 | 3.087 | 0.0405 |
| glnQ | Probable amino acid ABC transporter | CPE2092 | 2.263 | 0.0276 |
| Hypothetical protein | CPE2100 | 2.371 | 0.0276 | |
| Probable mercuric ion-binding protein | CPE2151 | 2.128 | 0.0276 | |
| lraI | Metal transport and potential adhesin | CPE2158 | 2.531 | 0.0276 |
| nlpD | Membrane protein related to metalloendopeptidase | CPE2182 | 2.322 | 0.0480 |
| lepW | Signal peptidase type I | CPE2295 | 2.761 | 0.0405 |
| add | Probable adenosine deaminase | CPE2506 | 3.538 | 0.0276 |
| Conserved hypothetical protein with CXXC pairs | CPE2549 | 4.434 | 0.0276 | |
| lpd | Probable oxidoreductase | CPE2550 | 3.875 | 0.0276 |
| glpA | Glycerol-3-phosphate dehydrogenase | CPE2551 | 2.652 | 0.0276 |
| glpP | Probable glycerol uptake operon antiterminator | CPE2553 | 2.101 | 0.0276 |
| agaS | Probable tagatose-6-phosphate aldose/ketose isomerase | CPE2625 | 2.114 | 0.0405 |
| gatY | Probable tagatose-bisphosphate aldolase | CPE2626 | 2.311 | 0.0276 |
| manY | Probable PTS system | CPE2631 | 2.527 | 0.0405 |
| Genes transcribed at higher levels in liquid than on plates | ||||
| Predicted membrane protein in amiC operon | CPE0117 | 2.138 | 0.0276 | |
| mscL | Large-conductance mechanosensitive channel | CPE0174 | 2.349 | 0.0276 |
| adh | Alcohol dehydrogenase | CPE0449 | 3.342 | 0.0276 |
| opuBA | Glycine betaine/carnitine/choline ABC transporter | CPE0557 | 3.320 | 0.0276 |
| hisJ | Amino acid ABC transporter | CPE0600 | 2.705 | 0.0502 |
| hisM | Amino acid ABC transporter | CPE0601 | 2.959 | 0.0405 |
| glnQ | Amino acid ABC transporter | CPE0602 | 3.759 | 0.0276 |
| argG | Argininosuccinate synthase | CPE0691 | 3.140 | 0.0405 |
| Hypothetical protein, alone in operon | CPE0768 | 2.107 | 0.0276 | |
| pfs | 5′-methylthioadenosine/S-adenosylhomocysteine nuclosidase | CPE1050 | 4.068 | 0.0276 |
| cfa | Cyclopropane-fatty-acyl-phospholipid synthase | CPE1051 | 2.711 | 0.0276 |
| sseA | Thiosulfate sulfur transferase | CPE1052 | 2.314 | 0.0276 |
| adeC | Adenine deaminase | CPE1268 | 2.032 | 0.0276 |
| potD | Spermidine/putrescine-binding protein | CPE1269 | 2.464 | 0.0276 |
| nupC | Pyrimidine nucleoside transporter | CPE1284 | 3.637 | 0.0276 |
| Hypothetical protein, alone in operon | CPE1539 | 3.105 | 0.0276 | |
| Conserved hypothetical protein | CPE1655 | 2.296 | 0.0405 | |
| Probable xanthine/uracil/vitamin C permease | CPE1751 | 2.101 | 0.0276 | |
| abrB | Stage V sporulation protein T, transcritional regulator | CPE2482 | 3.013 | 0.0276 |
| adhE | Aldehyde-alcohol dehydrogenase E | CPE2531 | 2.187 | 0.0276 |
| spmB | Spore maturation protein B | CPE2532 | 2.263 | 0.0405 |
| glnA | Glutamine synthetase | CPE2569 | 2.216 | 0.0405 |
| Conserved hypothetical protein, alone in operon | CPE2585 | 3.485 | 0.0276 | |
a. DGE (LFC), differential gene expression (log fold change). Calculated from the TPM from 6 samples grown on plates versus 6 samples grown in liquid