TABLE 6.
Genes positively regulated by σB in lineage II but not in lineage I
| Genea | Productb | Fold changec |
Adjusted P valued |
||
|---|---|---|---|---|---|
| Lineage I | Lineage II | Lineage I | Lineage II | ||
| lmo0019 | Conserved hypothetical protein | 1.4 | 2.9 | 0.1649 | 0.0000 |
| lmo0043 | Similar to arginine deiminase | 1.9 | 3.7 | 0.3567 | 0.0000 |
| lmo0135 | Oligopeptide ABC transporter, oligopeptide-binding protein | 0.8 | 2.0 | 0.2953 | 0.0000 |
| lmo0136 | Oligopeptide ABC transporter, permease protein | 0.6 | 1.5 | 0.1425 | 0.0000 |
| lmo0264 | Internalin C2 | 1.6 | 5.3 | 0.3567 | 0.0000 |
| lmo0265 | Peptidase, M20/M25/M40 family | 1.5 | 8.2 | 0.7760 | 0.0000 |
| lmo0292 | Similar to heat shock protein HtrA serine protease | 1.4 | 1.6 | 0.1117 | 0.0017 |
| lmo0321 | Similar to unknown proteins | 3.5 | 5.3 | 0.1010 | 0.0000 |
| lmo0342 | Similar to transketolase | 1.5 | 1.6 | 0.5712 | 0.0185 |
| lmo0343 | Similar to transaldolase | 1.1 | 2.0 | 0.9782 | 0.0011 |
| lmo0344 | Similar to dehydrogenase/reductase | 1.3 | 1.8 | 0.8013 | 0.0083 |
| lmo0345 | Similar to sugar phosphate isomerase | 1.3 | 1.5 | 0.8159 | 0.0002 |
| lmo0346 | Similar to triosephosphate isomerase | 1.3 | 1.9 | 0.8578 | 0.0062 |
| lmo0348 | Dihydroxyacetone kinase | 1.2 | 1.8 | 0.9272 | 0.0098 |
| lmo0398 | Similar to phosphotransferase system enzyme IIA | 0.7 | 13.5 | 0.1649 | 0.0000 |
| lmo0399 | PTS IIABC component, degenerate | 0.9 | 10.5 | 0.8049 | 0.0000 |
| lmo0400 | PTS IIABC component, degenerate | 1.0 | 20.5 | 0.9922 | 0.0000 |
| lmo0401 | Glycosyl hydrolase, family 38 | 0.8 | 13.4 | 0.3601 | 0.0000 |
| lmo0402 | Similar to transcriptional antiterminator (BglG family) | 1.5 | 15.7 | 0.1404 | 0.0000 |
| lmo0439 | Conserved hypothetical protein | 3.8 | 5.6 | 0.1291 | 0.0000 |
| lmo0449 | Unknown | 1.7 | 1.5 | 0.4564 | 0.0238 |
| lmo0584 | Conserved hypothetical membrane protein | 1.2 | 1.7 | 0.3709 | 0.0001 |
| lmo0589 | Unknown | 1.7 | 1.7 | 0.1977 | 0.0079 |
| lmo0590 | Similar to a fusion of two types of conserved hypothetical proteins, conserved hypothetical | 1.1 | 1.7 | 0.9228 | 0.0003 |
| lmo0591 | Membrane protein, putative | 1.2 | 1.5 | 0.4479 | 0.0166 |
| lmo0626 | Similar to unknown protein | 1.4 | 2.0 | 0.8736 | 0.0005 |
| lmo0628 | Unknown | 2.9 | 3.3 | 0.2091 | 0.0000 |
| lmo0647 | Unknown | 1.4 | 2.0 | 0.1241 | 0.0003 |
| lmo0648 | Magnesium transporter, CorA family | 1.7 | 1.7 | 0.2015 | 0.0014 |
| lmo0649 | Transcriptional regulator, GntR family | 2.7 | 1.7 | 0.1298 | 0.0004 |
| lmo0650 | Conserved membrane protein | 1.8 | 1.9 | 0.0763 | 0.0000 |
| lmo0759 | Glyoxalase family protein | 0.8 | 1.6 | 0.5762 | 0.0049 |
| lmo0760 | Unknown | 0.9 | 1.6 | 0.5681 | 0.0016 |
| lmo0811 | Carbonic anhydrase | 1.7 | 1.7 | 0.1107 | 0.0002 |
| lmo0818 | Cation transport ATPase, E1-E2 family | 0.7 | 1.7 | 0.4525 | 0.0023 |
| lmo0819 | Unknown | 1.5 | 1.7 | 0.0833 | 0.0010 |
| lmo0928 | Similar to 3-methyladenine DNA glycosylase | 2.0 | 1.5 | 0.1498 | 0.0150 |
| lmo0929 | Sortase family protein | 1.8 | 1.6 | 0.0663 | 0.0032 |
| lmo0995 | Membrane protein, putative | 1.1 | 3.4 | 0.9752 | 0.0001 |
| lmo1037 | B. subtilis YoaT protein homolog lmo1037 (imported) | 1.0 | 1.6 | 0.9873 | 0.0064 |
| lmo1064 | Hypothetical protein | 1.4 | 1.7 | 0.7066 | 0.0002 |
| lmo1072 | Highly similar to pyruvate carboxylase | 1.2 | 1.5 | 0.5247 | 0.0062 |
| lmo1121 | Unknown | 1.9 | 2.4 | 0.0539 | 0.0000 |
| lmo1226 | Similar to transporter (to B. subtilis YdgH protein) | 1.2 | 1.5 | 0.5341 | 0.0023 |
| lmo1242 | B. subtilis YdeI protein homolog lin1206 | 1.1 | 1.6 | 0.8038 | 0.0004 |
| lmo1243 | Uncharacterized conserved protein, PhnB family CAC3689 | 0.9 | 1.5 | 0.8989 | 0.0117 |
| lmo1360 | Highly similar to methylene tetrahydrofolate dehydrogenase and methenyl tetrahydrofolate cyclohydrolase | 1.6 | 1.6 | 0.1421 | 0.0017 |
| lmo1388 | CD4 T-cell-stimulating antigen, lipoprotein | 1.6 | 1.7 | 0.1146 | 0.0066 |
| lmo1421 | Similar to glycine betaine/carnitine/choline ABC transporter (ATP-binding protein) | 1.7 | 2.2 | 0.1477 | 0.0003 |
| lmo1426 | Similar to glycine betaine/carnitine/choline ABC transporter (osmoprotectant-binding protein) | 1.8 | 3.1 | 0.0541 | 0.0000 |
| lmo1427 | Glycine betaine/l-proline ABC transporter, permease protein | 1.3 | 3.0 | 0.4386 | 0.0000 |
| lmo1527 | Similar to protein export membrane protein SecDF | 1.8 | 1.5 | 0.1750 | 0.0006 |
| lmo1534 | l-Lactate dehydrogenase | 1.5 | 1.6 | 0.1649 | 0.0005 |
| lmo1571 | 6-Phosphofructokinase | 1.4 | 1.5 | 0.3590 | 0.0001 |
| lmo1580 | Universal stress protein family | 1.3 | 2.0 | 0.2022 | 0.0000 |
| lmo1622 | Conserved hypothetical protein | 1.2 | 1.6 | 0.5714 | 0.0011 |
| lmo1635 | Conserved hypothetical protein | 2.1 | 1.7 | 0.1056 | 0.0037 |
| lmo1637 | Putative ABC transporter, permease protein | 1.4 | 1.6 | 0.2716 | 0.0002 |
| lmo1666 | Conserved hypothetical protein | 1.4 | 1.6 | 0.7464 | 0.0002 |
| lmo1681 | Similar to cobalamin-independent methionine synthase | 1.2 | 1.5 | 0.7274 | 0.0061 |
| lmo1636 | Similar to ABC transporter (ATP-binding protein) | 2.0 | 1.9 | 0.0936 | 0.0001 |
| lmo1696 | Putative membrane protein | 1.2 | 1.5 | 0.4402 | 0.0073 |
| lmo1698 | Acetyltransferase, GNAT family | 1.1 | 3.5 | 0.8156 | 0.0001 |
| lmo1702 | Glyoxalase family protein | 1.0 | 1.6 | 0.9402 | 0.0369 |
| lmo1713 | Cell shape-determining protein | 1.5 | 1.5 | 0.4402 | 0.0244 |
| lmo1749 | Similar to shikimate kinase | 1.5 | 1.9 | 0.5157 | 0.0003 |
| lmo1790 | Metallo-beta-lactamase family protein | 1.5 | 1.7 | 0.2399 | 0.0001 |
| lmo1806 | Highly similar to acyl carrier proteins | 1.2 | 1.9 | 0.7644 | 0.0000 |
| lmo1883 | Chitinase | 2.6 | 3.2 | 0.3466 | 0.0000 |
| lmo1929 | Similar to nucleoside diphosphate kinase | 1.1 | 1.8 | 0.9873 | 0.0001 |
| lmo1930 | Heptaprenyl diphosphate synthase component II (imported) | 2.2 | 1.6 | 0.1056 | 0.0003 |
| lmo1931 | 2-Heptaprenyl-1,4-naphthoquinone methyltransferase | 1.9 | 1.8 | 0.0763 | 0.0002 |
| lmo1932 | Heptaprenyl diphosphate synthase component I, putative | 1.8 | 1.5 | 0.1616 | 0.0272 |
| lmo1933 | Similar to GTP cyclohydrolase I | 2.2 | 1.9 | 0.5761 | 0.0002 |
| lmo2031 | Conserved hypothetical protein TIGR00044 | 1.2 | 1.6 | 0.4204 | 0.0111 |
| lmo2033 | Highly similar to cell division protein FtsA | 1.4 | 1.6 | 0.2091 | 0.0015 |
| lmo2159 | Oxidoreductase, Gfo/Idh/MocA family | 1.3 | 3.4 | 0.3295 | 0.0000 |
| lmo2160 | AP endonuclease family 2 C terminus family | 1.5 | 2.8 | 0.0988 | 0.0000 |
| lmo2161 | ThuA protein | 1.7 | 2.2 | 0.1642 | 0.0000 |
| lmo2162 | Conserved hypothetical protein | 1.6 | 2.1 | 0.1513 | 0.0001 |
| lmo2169 | Unknown | 1.4 | 1.7 | 0.2512 | 0.0000 |
| lmo2196 | Similar to pheromone ABC transporter (binding protein) | 0.9 | 1.6 | 0.9436 | 0.0006 |
| lmo2230 | Similar to arsenate reductase | 10.5 | 18.7 | 0.0947 | 0.0000 |
| lmo2231 | Similar to unknown proteins | 0.9 | 3.1 | 0.9720 | 0.0009 |
| lmo2368 | MutT/nudix family protein | 1.6 | 1.5 | 0.0577 | 0.0054 |
| lmo2386 | Similar to B. subtilis YuiD protein | 1.1 | 1.9 | 0.9436 | 0.0000 |
| lmo2387 | Conserved hypothetical protein | 1.4 | 4.0 | 0.3857 | 0.0000 |
| lmo2389 | Similar to NADH dehydrogenase | 1.9 | 1.8 | 0.1056 | 0.0000 |
| lmo2399 | Similar to conserved hypothetical proteins | 1.5 | 1.8 | 0.2577 | 0.0004 |
| lmo2437 | Conserved hypothetical protein | 1.0 | 2.0 | 0.9866 | 0.0000 |
| lmo2465 | Conserved hypothetical protein | 1.5 | 1.8 | 0.3884 | 0.0000 |
| lmo2511 | Similar to conserved hypothetical proteins like B. subtilis YvyD protein | 1.2 | 1.9 | 0.5123 | 0.0001 |
| lmo2520 | N-Acylamino acid racemase | 0.8 | 1.8 | 0.6061 | 0.0000 |
| lmo2522 | Similar to hypothetical cell wall-binding protein from B. subtilis | 1.0 | 1.6 | 0.9825 | 0.0028 |
| lmo2534 | ATP synthase F0, C subunit | 1.4 | 1.5 | 0.1426 | 0.0006 |
| lmo2536 | Highly similar to ATP synthase subunit i | 1.4 | 1.6 | 0.2900 | 0.0009 |
| lmo2568 | Unknown | 1.4 | 1.6 | 0.6145 | 0.0236 |
| lmo2611 | Adenylate kinase | 1.0 | 1.5 | 0.9866 | 0.0143 |
| lmo2638 | Pyridine nucleotide-disulfide oxidoreductase family protein | 1.0 | 1.5 | 0.9914 | 0.0025 |
| lmo2670 | Hypothetical protein | . | 2.3 | NA | 0.0000 |
| lmo2695 | Dihydroxyacetone kinase, Dak1 subunit, putative | 1.6 | 1.6 | 0.1042 | 0.0003 |
| lmo2696 | Dihydroxyacetone kinase family protein | 1.5 | 1.8 | 0.1100 | 0.0001 |
| lmo2720 | Acetyl-coenzyme A synthetase | 1.0 | 1.5 | 0.9951 | 0.0022 |
| lmo2739 | Transcriptional regulator, Sir2 family | 1.7 | 1.5 | 0.0538 | 0.0038 |
| lmo2741 | Major facilitator family transporter | 1.7 | 1.5 | 0.0698 | 0.0010 |
| lmo2742 | SH3 domain protein | 0.7 | 1.5 | 0.1447 | 0.0015 |
| lmo2832 | Glycerate kinase 2 | 1.2 | 1.5 | 0.8437 | 0.0083 |
| lmof2365_1394 | Hypothetical protein | 1.9 | 1.5 | 0.1498 | 0.0068 |
a
Gene names are based on the L. monocytogenes EGDe locus. Bold type indicates putative operons.
b
Common names of the products are based on the EGDe annotation.
c
Changes in the transcript level in the parent strain compared to the transcript level in the ΔsigB strain. A ≥1.5-fold change was considered significant.
d
An adjusted P value of <0.05 was considered significant.