Table 1.
Genes up- and down-regulated in UA159 and fabM::Erm during glucose-shock and steady-state growth. This table includes genes commented on in the text. The complete dataset is available in Supplementary Tables S1–S7. Statistically significant changes in expression are given as a ratio of the first strain/condition listed versus the 2nd strain/condition listed. Data is grouped according to functional class. Number in parenthesis (where applicable) indicates value for comparison calculated from other available comparisons. ‘SS’ = steady-state; ‘GS’ = glucose-shock.
| Comparison # | 1 | 2 | 4 | 6 | 3 | 5 | 7 | ||
|---|---|---|---|---|---|---|---|---|---|
|
| |||||||||
| Gene | Locus | Description | fabM::Erm SS 7 vs UA159 SS 7 | UA159 GS vs. SS 7 | UA159 SS 5 vs. GS | UA159 SS 5 vs. SS 7 | fabM::Erm GS vs. SS 7 | fabM::Erm SS 5.5 vs. GS | fabM::Erm SS 5.5 vs. SS 7 |
| Oxidative Stress | |||||||||
| sod | SMU.629 | superoxide dismutase | 8.809 | 0.256 | (2.25) | 2.891 | |||
| ahpC | SMU.764 | alkyl hydroperoxide reductase | 2.41 | 13.46 | 0.211 | 2.84 (2.84) | |||
| ahpF | SMU.765 | H2O2-forming NADH oxidase | 12.397 | 0.242 | 3.00 (3.00) | 3.058 | |||
| tpx | SMU.924 | thiol peroxidase | 3.141 | 9.811 | 0.307 | (3.01) | 2.983 | ||
| gor | SMU.838 | glutathione oxidoreductase | 3.982 | 8.894 | 0.295 | (2.62) | 4.481 | ||
| dpr | SMU.540 | peroxide resistance protein | 2.429 | 0.375 | (0.91) | 3.442 | |||
| Amino Acid Biosynthesis | |||||||||
| glnA | SMU.364 | glutamine synthase | 2.857 | 0.345 | (0.99) | ||||
| proC | SMU.1974 | pyrroline carboxylate reductase | 2.2 | 0.382 | |||||
| hisA | SMU.1265 | ProFAR | 4.025 | 2.01 | |||||
| hisB | SMU.1268 | IGPD | 2.843 | 0.250 | |||||
| ilvE | SMU.1203 | BCAA aminotransferase | 2.391 | 4.571 | 3.521 | 2.19 | 0.417 | ||
| ilvB | SMU.231 | acetolactate synthase, large subunit | 2.718 | 0.480 | |||||
| ilvC | SMU.233 | ketol-acid reductoisomerase | |||||||
| nifS | SMU.249 | class-V aminotransferase | 3.677 | 0.381 | (1.40) | 2.255 | |||
| cysK | SMU.496 | cysteine synthetase | 2.848 | 3.035 | 0.313 | ||||
| cysD | SMU.1173 | O-acetylhomoserine sulfhydrylase | 1.894 | 1.877 | |||||
| hisF | SMU.1264 | imidazoleglycerol-phosphate synthase | 2.542 | 0.352 | (0.895) | ||||
| argJ | SMU.664 | ornithine acetyltransferase | 0.44 | ||||||
| Toxin Production and Resistance | |||||||||
| bip | SMU.1914c | 12.916 | 74.647 | 117 | 4.454 | 7.97 | |||
| SMU.1906c | 12.204 | 118.112 | 169.786 | 7.016 | 7.93 | ||||
| SMU.423 | 5.165 | 46.787 | 48.724 | 6.809 | |||||
| DNA Repair | |||||||||
| mutY | SMU.1865 | A/G-specific DNA glycosylase | 3.4 | 0.312 | (1.06) | 3.374 | |||
| smn (end3) | SMU.1650 | endonuclease III | 6.755 | 0.304 | (2.06) | 3.214 | |||
| Nucleotide Synthesis | |||||||||
| purB | SMU.59 | adenylosuccinate lyase | 0.220 | 0.36 | |||||
| purL | SMU.30 | FGAM synthase | 2.44 | 12.676 | 6.342 | ||||
| purD | SMU.48 | GARS | 2.672 | ||||||
| purF | SMU.32 | PPAT | 6.066 | 4.659 | |||||
| purM | SMU.34 | AIRS | 8.39 | 4.632 | 0.290 | ||||
| purN | SMU.35 | GART | 5.714 | 0.258 | |||||
| pyrB | SMU.858 | aspartate transcarbamoylase | 6.68 | 0.150 | (1.00) | ||||
| pyrA | SMU.859 | carbamoyl phosphate synthetase | 14.654 | 0.104 | (1.52) | ||||
| pyrAB | SMU.860 | carbamoyl phosphate synthetase | 9.405 | 0.115 | (1.09) | ||||
| pyrD | SMU.595 | dihydroorotate dehydrogenase | 3.778 | 5.206 | 3.691 | ||||
| pyrE | SMU.1221 | orotate phosphoribosyltransferase | 5.128 | 0.117 | (0.60) | ||||
| pyrF | SMU.1222 | orotidine-5-decarboxylase | 5.711 | 0.144 | (0.82) | ||||
| pyrDB | SMU.1223 | dihydroorotate dehydrogenase | 5.877 | 0.089 | (0.53) | 0.409 | |||
| pyrK | SMU.1224 | dihydroorotate dehydrogenase | 37.417 | 0.029 | (1.10) | ||||
| fhs | SMU.1073 | formyl-tetrahydrofolate synthetase | 4.277 | 1.963 | |||||
| Two-Component Systems | |||||||||
| comD | SMU.1916 | HK of competence regulon | 7.47 | 3.341 | |||||
| comE | SMU.1917 | RR of the competence regulon | 8.176 | ||||||
| ciaR | SMU.1129 | response regulator | 6.733 | ||||||
| PTS | |||||||||
| EI | SMU.675 | general PTS EI protein | 0.341 | ||||||
| ptsH | SMU.674 | general PTS histidine protein | 0.363 | ||||||
| bglP | SMU.980 | beta-glucoside-specific EII component | 3.037 | 0.11 | 10.841 | (1.193) | 0.356 | ||
| scrA | SMU.1841 | sucrose-specific IIABC component | 0.188 | 0.491 | |||||
| manL | SMU.1877 | mannose-specific component IIAB | 0.353 | 0.147 | 2.969 | ||||
| manM | SMU.1878 | mannose-specific component IIC | 0.387 | 0.162 | 2.863 | (0.464) | |||
| pttB | SMU.2038 | trehalose-specific IIABC component | 0.149 | 0.236 | |||||
| ptcC | SMU.1596 | cellobiose-specific IIC component | 6.058 | 0.435 | 0.265 | ||||
| ptsG | SMU.2047 | glucose-specific IIABC component | 0.353 | 0.214 | |||||
| pthP | SMU.754 | HPr kinase/phosphatase | 2.807 | ||||||
| Transport & Binding | |||||||||
| trk | SMU.1562 | potassium uptake protein | 4.655 | 3.075 | 3.63 | ||||
| trkA | SMU.1708 | potassium uptake protein | 2.585 | 2.661 | 3.212 | ||||
| trkB | SMU.1561 | potassium uptake protein | 3.447 | 2.486 | 3.678 | ||||
| trkH | SMU.1709 | potassium uptake protein | 2.914 | ||||||
| copA | SMU.426 | copper transporting ATPase | 8.104 | 3.125 | 5.023 | ||||
| copZ | SMU.427 | copper chaperone | 8.271 | 3.085 | 2.804 | ||||
| sloA | SMU.182 | ABC transporter | 0.157 | 0.192 | 0.190 | 0.223 | |||
| sloB | SMU.183 | Mn/Zn ABC transporter | 0.203 | 0.288 | 0.107 | 0.15 | |||
| sloC | SMU.184 | metal-binding ABC transporter | 0.345 | 2.202 | 0.147 | 0.324 (0.32) | 0.313 | 0.361 | |
| malF | SMU.1569 | maltose/maltodextrin ABC transporter | 0.421 | 0.385 | |||||
| malX | SMU.1568 | maltose/maltodextrin ABC transporters | 0.162 | 0.317 | |||||
| malG | SMU.1570 | maltose/maltodextrin ABC transporters | 0.389 | ||||||
| msmE | SMU.878 | MSM sugar-binding protein precursor | 6.351 | 6.615 | |||||
| msmF | SMU.879 | MSM permease protein | 4.270 | 3.714 | |||||
| msmG | SMU.880 | MSM permease preotein | 3.852 | 3.595 | 2.026 | ||||
| msmK | SMU.882 | MSM ATP-binding protein | 3.667 | 3.326 | |||||
| Replication and Cell Division | |||||||||
| ssb | SMU.1859 | single-stranded DNA-binding protein | 0.23 | 0.357 | 0.166 | 3.773 | (0.626) | ||
| dnaI | SMU.1921 | DNA replication protein primosome | 0.502 | 0.568 | |||||
| holB | SMU.1662 | DNA polymerase III, delta subunit | 0.348 | ||||||
| recJ | SMU.1472 | single-stranded DNA exonuclease | 0.268 | 2.942 | (0.788) | 0.175 | 3.354 | (0.587) | |
| rpoA | SMU.2001 | RNA polymerase, alpha subunit | 0.245 | 0.199 | 0.141 | 12.000 | (1.69) | ||
| ftsH | SMU.15 | cell division protein | 0.332 | 6.449 | |||||
| ftsX | SMU.1324 | cell division protein | 2.261 | 0.35 | |||||
| ftsQ | SMU.550 | cell division protein | |||||||
| ftsW | SMU.713 | cell division protein | 2.063 | 2.876 | 2.224 | ||||
| Protein Repair & Degradation | |||||||||
| clpE | SMU.562 | ATP-dependent protease | 2.821 | ||||||
| thdF | SMU.1235 | thioprene & furan degradation protein | 4.456 | 3.647 | |||||
| grpE | SMU.81 | heat shock protein (HSP-70) co-factor | 0.387 | 2.123 | 0.292 | (0.620) | 2.554 | ||
| clpB | SMU.1425 | Clp proteinase, ATP-binding subunit | 4.922 | ||||||
| Energy Metabolism | |||||||||
| pfk | SMU.1191 | phosphofructokinase | 2.977 | 1.806 | |||||
| gapN | SMU.676 | GAD-3-P dehydrogenase | 1.759 | 2.152 | |||||
| adhA | SMU.127 | acetoin dehydrogenase | 5.114 | 0.252 | (1.29) | 2.648 | |||
| adhB | SMU.128 | acetoin dehydrogenase | 6.335 | 0.246 | (1.56) | 7.386 | 4.328 | ||
| adhC | SMU.129 | dihydrolipoamide acetyltransferase | 7.334 | 0.230 | (1.69) | 8.811 | |||
| adhD | SMU.130 | dihydrolipoamide dehydrogenase | 11.891 | 0.222 | (2.64) | 9.068 | 4.05 | ||
| alsS | SMU.1452 | α-acetolactate synthase | 2.518 | 10.263 | 0.198 | (2.03) | 4.21 | 0.281 | (1.18) |
| aldB | SMU.1451 | α-acetolactate decarboxylase | 8.274 | 2.549 | |||||
| citB | SMU.670 | aconitate hydratase aconitase | 0.149 | 0.055 | 0.025 | 0.338 | 0.333 | ||
| citZ | SMU.671 | citrate synthase | 0.134 | 0.083 | 0.041 | ||||
| idh | SMU.672 | isocitrate dehydrogenase | 0.156 | 0.075 | 0.036 | 0.426 | |||
| nox | SMU.1117 | H2O2-forming NADH oxidase | 0.182 | 0.319 | 2.615 | (0.834) | |||
| glk | SMU.542 | glucose kinase | 0.411 | ||||||
| eno | SMU.1247 | enolase | 0.507 | 0.453 | 2.816 | (1.28) | |||
| pfkB | SMU.871 | fructose-1-P kinase | 0.167 | 4.048 | (0.676) | 2.269 | |||
| adhE | SMU.148 | alcohol/acetaldehyde dehydrogenase | 0.186 | 0.142 | |||||
| ackA | SMU.1978 | acetate kinase | 0.382 | ||||||
| scrB | SMU.1843 | sucrose-6-P hydrolase | 0.181 | 5.082 | (0.920) | ||||
| treA | SMU.2037 | trehalose-6-P hydrolase | 0.161 | 2.704 | (0.435) | 0.093 | 6.423 | (0.598) | |
| dex A | SMU.2042 | dextranase precursor | |||||||
| dex B | SMU.883 | dextran glucosidase | 3.689 | ||||||
| gtfA | SMU.881 | sucrose phosphorylase | 3.974 | ||||||
| pykF | SMU.1190 | pyruvate kinase | 2.507 | 2.182 | |||||
| pgk | SMU.361 | phosphoglycerate kinase | 3.318 | ||||||
| capP | SMU.712 | phosphoenolpyruvate carboxylase | 3.046 | ||||||
| gtfC | SMU.1005 | glucosyltransferase-SI | 0.386 | 6.047 | 2.205 | ||||
| pgm B | SMU.1747c | beta-phosphoglucomutase | 0.29 | ||||||
| citE | SMU.1020 | citrate lyase | 2.26 | ||||||
| ldh | SMU.1115 | lactate dehydrogenase | |||||||
| mleS | SMU.137 | malolactic enzyme | 12.874 | ||||||
| mleP | SMU.138 | malate permease | 5.778 | ||||||
| pfl | SMU.402 | pyruvate formate-lyase | |||||||
| glgD | SMU.1537 | glycogen biosynthesis protein | 0.194 | 4.567 | (0.886) | ||||
| glgC | SMU.1538 | glucose-1-P adenylyltransferase | 0.31 | 2.942 | (0.912) | ||||
| glgB | SMU.1539 | 1,4-alpha-glucan branching enzyme | 0.177 | 3.066 | (0.543) | ||||
| glgP | SMU.1564 | glycogen phosphorylase | 0.357 | 0.387 | |||||
| Cell Envelope | |||||||||
| spaP | SMU.610 | cell surface antigen | 6.012 | 2.704 | |||||
| mreC | SMU.20 | cell shape-determining protein | 0.104 | 7.711 | (0.802) | ||||
| mreD | SMU.21 | cell shape-determining protein | 0.287 | 3.438 | (0.987) | 0.34 | 3.459 | (1.18) | |
| dltC | SMU.1689 | putative D-alanyl carrier protein | 0.228 | 3.405 | (0.776) | 0.279 | |||
| dltD | SMU.1688 | putative extramembranal protein | 0.302 | 4.720 | (1.425) | ||||
| murC2 | SMU.1429 | UDP-N-acetylmuramyl tripeptide synthetase | 0.35 | ||||||
| pbp2a | SMU.1949 | carboxypeptidase | 0.366 | 5.880 | |||||
| pbp2x | SMU.455 | penicillin-binding protein 2X | 0.32 | 2.572 | (0.823) | 0.422 | 2.644 | (1.12) | |
| pgm A | SMU.1077 | alpha phosphoglucomutase | 0.247 | 4.449 | (1.099) | ||||
| mraY | SMU.456 | undecaprenyl-phosphate-UDP-MurNAc-pentapeptide transferase | 0.378 | 2.487 | (0.940) | ||||
| ffh | SMU.1060 | signal recognition particle protein | 0.355 | ||||||
| pbp1b | SMU.1991 | penicillin-binding protein 1 b | 0.417 | 2.929 | (1.22) | ||||
| thiD | SMU.85 | phosphomethylpyrimidine kinase | 4.511 | 2.362 | 0.288 | (0.68) | |||
| Fatty Acid Biosynthesis | |||||||||
| accA | SMU.1734 | acetyl-CoA carboxylase, alpha subunit | 0.324 | ||||||
| accD | SMU.1735 | acetyl-CoA carboxylase, beta subunit | 0.381 | 0.371 | 0.263 | 4.759 | (1.25) | ||
| fabZ | SMU.1737 | 3-hydroxymyristoyl-ACP dehydratase | 0.395 | 2.303 | |||||
| fabG | SMU.1740 | 3-oxoacyl-ACP reductase | 0.331 | ||||||
| fabD | SMU.1741 | malonyl-CoA (ACP) transacylase | 0.338 | 2.562 | |||||
| fabK | SMU.1742c | trans-2-enoyl-ACP reductase | 0.384 | 3.029 | |||||
| fabH | SMU.1744 | 3-oxoacyl-ACP synthase III | 0.314 | 0.351 | 3.400 | (1.19) | |||
| fabF | SMU.1739 | 3-oxylacyl-ACP-synthase | 0.481 | 2.097 | (1.01) | ||||
| acp | SMU.1743 | acyl carrier protein | 0.258 | 0.21 | |||||
| fabK2 | SMU.1335c | enoyl-ACP-reductase | 4.262 | ||||||
| cls | SMU.988 | cardiolipin synthase | 0.421 | 0.249 | 2.911 | (0.725) | |||
| Ribosome | |||||||||
| rs1 | SMU.1200 | putative ribosomal protein S1 | 0.275 | 0.409 | |||||
| rl1 | SMU.1626 | 50S ribosomal protein L1 | 0.341 | 2.831 | (0.97) | 0.363 | |||
| rl11 | SMU.1627 | 50S ribosomal L11 protein | 2.171 | 0.366 | |||||
| rs11 | SMU.2002 | 30S ribosomal protein S11 | 0.328 | 0.364 | 0.283 | 6.347 | (1.80) | ||
| rs13 | SMU.2003 | 30S ribosomal protein S13 | 0.23 | 0.265 | 11.605 | (3.08) | |||
| rs5 | SMU.2009 | 30S ribosomal protein S5 | 0.489 | 0.38 | 2.699 | (1.03) | 0.265 | 3.500 | (0.928) |
| rl18 | SMU.2010 | 50S ribosomal protein L18 | 0.39 | 2.189 | 0.366 | 3.994 | (1.46) | ||
| rl6 | SMU.2011 | 50S ribosomal protein L6 (BL10) | 0.415 | 0.38 | 0.418 | 5.677 | (2.37) | ||
| rs8 | SMU.2012 | 30S ribosomal protein S8 | 0.276 | 0.403 | 0.149 | 10.983 | (1.64) | ||
| rs14 | SMU.2014 | 30S ribosomal protein S14 | 0.471 | 0.428 | 5.719 | (2.45) | |||
| rl5 | SMU.2015 | 50S ribosomal protein L5 | 0.348 | 0.464 | 0.412 | 5.117 | (2.11) | ||
| rl24 | SMU.2016 | 50S ribosomal protein L24 | 0.331 | 0.303 | 3.662 | (1.11) | 0.252 | 10.765 | (2.71) |
| rl14 | SMU.2017 | 50S ribosomal protein L14 | 0.398 | 0.428 | 5.719 | (2.48) | |||
| rl29 | SMU.2019 | 50s ribosomal protein L29 | 0.335 | 0.274 | 0.242 | 8.009 | (1.94) | ||
| rl16 | SMU.2020 | 50S ribosomal protein L16 | 0.473 | 0.493 | 0.412 | 4.477 | (1.84) | ||
| rs2 | SMU.2032 | 30S ribosomal protein S2 | 0.512 | 0.45 | |||||
| F1F0 ATPase | |||||||||
| atpA | SMU.1527 | epsilon subunit | 2.468 | 2.538 | 2.609 | ||||
| atpB | SMU.1528 | beta subunit | 2.968 | 3.327 | 2.456 | ||||
| atpC | SMU.1529 | gamma subunit | 2.343 | 2.386 | 2.937 | ||||
| atpD | SMU.1530 | alpha subunit | 2.488 | 2.779 | 2.121 | 2.825 | |||
| atpE | SMU.1531 | delta subunit | 2.271 | ||||||
| atpF | SMU.1532 | b subunit | 3.050 | 2.626 | 3.20 | ||||
| atpG | SMU.1533 | a subunit | 3.109 | 2.452 | 3.555 | 2.942 | |||
| atpH | SMU.1534 | c subunit | 3.228 | 2.978 | 3.909 | 2.954 | |||
| Transcriptional Regulators | |||||||||
| sloR | SMU.186 | metal-dependent transcriptional regulator | 0.150 | 0.537 | |||||
| glnR | SMU.363 | glutamine synthase regulator | 2.879 | 0.218 | (0.628) | ||||
| copY | SMU.424 | regulator of the copper operon | 15.129 | 4.779 | 3.545 | ||||
| furR | SMU.593 | ferric uptake regulator protein | 2.853 | ||||||
| malR | SMU.1566 | maltose operon regulator | 2.841 | ||||||
| fabT | SMU.1745c | regulator of the fab operon | 0.365 | ||||||
| ccpA | SMU.1591 | carbon catabolite control protein | 0.319 | ||||||
| brpA | SMU.410 | transcriptional regulator | 0.412 | 0.445 | |||||
| treR | SMU.2040 | regulator of the trehalose operon | 0.19 | ||||||
| spxA1 | SMU.1142c | redox regulator | 0.527 | ||||||
| spxA2 | SMU.2084c | redox regulator | 5.546 | ||||||
| codY | SMU.1824 | GTP binding transcriptional regulator | 0.372 | ||||||
| fruR | SMU.870 | regulator of fructose metabolism | 0.244 | 3.085 | |||||
| pyrR | SMU.856 | regulator of the pyrimidine operon | 7.095 | 0.075 | (0.532) | ||||
| cysR | SMU.852 | regulator of cysteine biosynthesis | 6.849 | ||||||
| cpsY | SMU.1225 | transcriptional regulator | 2.249 | 0.343 | |||||
| yhcF | SMU.1193 | transcriptional regulator | 5.510 | ||||||
| hrcA | SMU.80 | transcriptional regulator | 0.165 | 0.254 | 2.841 | ||||
| dnaA | SMU.01 | chromosomal replication initiator protein | 5.492 | ||||||
| rggD | SMU.1509 | transcriptional regulator | 3.524 | ||||||