Table 5.
Summary of genes up-regulated by σB
| Locus | EGD-e locus | Description | Avg. fold change (WT/ΔsigB)a | 10403S Average GEIb | ΔsigB Average GEIc |
|---|---|---|---|---|---|
| σB-dependent genes found by RNA-Seq and not previously identified by microarray analyses of stationary phase cells | |||||
| LMRG_02371 | lmo0122 | similar to phage proteins | 3.9 | 2.37 | 0.6 |
| LMRG_02611 | lmo0265 | similar to succinyldiaminopimelate desuccinylase | 204.5 | 17.95 | 0 |
| LMRG_02602 | lmo0274 | unknown | 3.17 | 2.89 | 0.91 |
| LMRG_00064 | lmo0372 | similar to beta-glucosidase | 4.26 | 2.4 | 0.66 |
| LMRG_00126d | lmo0433 (inlA) | Internalin A | 5.86 | 6.19 | 1.06 |
| LMRG_00127d | lmo0434 (inlB) | Internalin B | 6 | 2.71 | 0.47 |
| LMRG_02244 | lmo0819 | unknown | 3.01 | 18.35 | 6.09 |
| LMRG_00873d | lmo1421 | similar to glycine betaine/carnitine/choline ABC transporter (ATP-binding protein) | 28.44 | 5.27 | 0.67 |
| LMRG_00877d | lmo1425 (opuCD) | similar to betaine/carnitine/choline ABC transporter (membrane p) | 3.56 | 22.59 | 6.51 |
| LMRG_00878d | lmo1426 (opuCC) | similar to glycine betaine/carnitine/choline ABC transporter (osmoprotectant-binding protein) | 3.77 | 19.78 | 5.41 |
| LMRG_01013 | lmo1866 | similar to conserved hypothetical proteins | 2.63 | 4.87 | 1.79 |
| LMRG_01151 | lmo2003 | similar to transcription regulator GntR family | 14.67 | 3.15 | 0.32 |
| LMRG_01963 | lmo2733 | similar to PTS system, fructose-specific IIABC component | 7.95 | 1.35 | 0.32 |
| Noncoding | ND | putative ncRNA, sbrE | 186.09 | 2359.89 | 20.95 |
| σB-dependent genes with Average GEI ≥ 25 in 10403S | |||||
| Noncoding | ND | rliA (sbrE) | 186.09 | 2359.89 | 20.95 |
| LMRG_01674 | lmo2158 | similar to B. subtilis YwmG protein | 479.39 | 509.23 | 22.8 |
| LMRG_01365 | lmo1602 | similar to unknown proteins | 5.47 | 157.02 | 30.08 |
| LMRG_00221 | lmo0539 | similar to tagatose-1,6-diphosphate aldolase | 14.54 | 132.74 | 9.3 |
| LMRG_01602 | lmo2230 | similar to arsenate reductase | 411 | 96.43 | 0 |
| LMRG_02052 | lmo0953 | unknown | 167 | 73.18 | 0.48 |
| LMRG_00357 | lmo0669 | similar to oxidoreductase | 75.93 | 64.6 | 0.89 |
| LMRG_00358 | lmo0670 | unknown | 105.5 | 59.6 | 0.58 |
| LMRG_00341 | lmo0654 | unknown | 7.1 | 56.61 | 7.94 |
| LMRG_02219 | lmo2674 | similar to ribose 5-phosphate epimerase | 5.42 | 52.93 | 9.94 |
| LMRG_01794 | lmo2454 | unknown | 84.5 | 50.24 | 0.76 |
| LMRG_01850 | lmo2398 (ltrC) | low temperature requirement C protein, also similar to B. subtilis YutG protein | 2.8 | 50.03 | 18.94 |
| LMRG_00745 | lmo1295(hfq) | similar to host factor-1 protein | 4.83 | 49.77 | 11.19 |
| LMRG_01948 | lmo2748 | similar to B. subtilis stress protein YdaG | 207.5 | 49.37 | 0 |
| LMRG_00583 | lmo1140 | unknown | 11.93 | 47.84 | 4.28 |
| LMRG_02036 | lmo0937 | unknown | 54.38 | 44.68 | 0.91 |
| LMRG_00484 | lmo0796 | conserved hypothetical protein | 4.21 | 43.88 | 10.61 |
| LMRG_02772 | lmo1698 | similar to ribosomal-protein-alanine N-acetyltransferase | 4.1 | 42.94 | 10.92 |
| LMRG_02736 | lmo2391 | conserved hypothetical protein similar to B. subtilis YhfK protein | 11.76 | 39.48 | 4.54 |
| LMRG_02011 | lmo0911 | unknown | 4.04 | 33.9 | 8.58 |
| LMRG_01763 | lmo2485 | similar to B. subtilis yvlC protein | 3.93 | 32.87 | 8.47 |
| LMRG_00482 | lmo0794 | similar to B. subtilis YwnB protein | 67.02 | 32.5 | 0.72 |
| LMRG_00278 | lmo0596 | similar to unknown proteins | 170.5 | 32.33 | 0.09 |
| LMRG_02218 | lmo2673 | conserved hypothetical protein | 150.5 | 31.92 | 0.11 |
| LMRG_02013 | lmo0913 | similar to succinate semialdehyde dehydrogenase | 330.38 | 30.05 | 0.11 |
| LMRG_00469 | lmo0781 | similar to mannose-specific phosphotransferase system (PTS) component IID | 59.58 | 29.59 | 0.65 |
| LMRG_00470 | lmo0782 | similar to mannose-specific phosphotransferase system (PTS) component IIC | 18.99 | 29.59 | 1.58 |
| LMRG_01360 | lmo1606 | similar to DNA translocase | 7.88 | 29.5 | 3.97 |
| LMRG_02696 | lmo2572 | similar to Chain A, Dihydrofolate Reductase | 8.05 | 29.05 | 3.59 |
| LMRG_02768 | lmo1694 | similar to CDP-abequose synthase | 155.31 | 27.51 | 0.2 |
| LMRG_02216 | lmo2671 | unknown | 3.13 | 27.29 | 8.82 |
| LMRG_02695 | lmo2573 | similar to zinc-binding dehydrogenase | 7.52 | 25.91 | 3.83 |
| LMRG_00472 | lmo0784 | similar to mannose-specific phosphotransferase system (PTS) component IIA | 88.5 | 25.25 | 0.21 |
| LMRG_02215 | lmo2670 | conserved hypothetical protein | 3 | 25.23 | 8.58 |
| LMRG_02697 | lmo2571 | similar to nicotinamidase | 9.84 | 25.15 | 2.99 |
aAverage fold changes from the 10403S and ΔsigB. Genes with no matching reads in ΔsigB had their GEI set to 1 to allow for calculation of the fold change;
bAverage normalized number of reads matching each of the σB-dependent genes in the two 10403S datasets relative to the length of the genes times 100 bp;
cAverage normalized number of reads matching each of the σB-dependent genes in the two ΔsigB datasets relative to the length of the genes times 100 bp;
dGenes previously identified as σB-dependent under salt stress in L. monocytogenes10403S by Raengpradub et al., 2008.