Table 5 |
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|
Summary of genes up-regulated by σB |
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|
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 |
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|
|
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|
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 |
|
|
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|
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. |
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|
Oliver et al. BMC Genomics 2009 10:641 doi:10.1186/1471-2164-10-641 |
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