TABLE 2.
Summary of genes with σB-dependent expression patterns as identified by microarray analyses
| Category | Gene | Function or closest homologuea (E value) | Predicted σB promoter sequenceb | B. subtilis homologuec (E value) | Changed (fold)
|
|
|---|---|---|---|---|---|---|
| ST | OS | |||||
| Stress | lmo2230 | Arsenate reductase [Staphylococcus aureus] (le-08) | TTTAATGTTTCTAGTAATTTAAAAAGGGTAGATATTACTGT-N108-ATG | arsC (7e-10) | 27.0 | 21.9 |
| gadB | GadB glutamate decarboxylase (Lmo2434) | TGAACGGTTTGTCTCTGTGGTTTAATGGGTATTGGTGAGAGA-N32-ATG | 5.3 | 4.9 | ||
| sepA | Metallo-beta-lactamase superfamily protein [Shewanella oneidensis] (e-173) | CAAAAGGTTTTGAATAATTTTATGGAGGTATAAAAAGAAAGT-N33-ATG | 12.0 | 13.4 | ||
| ltrC | Low-temperature-requirement C protein | CCGTCCGTTTTTAGTTCGTGATGGCGGGGACTATGAACTTAT-N260-ATG† | yutG (le-53)‡ | 4.8 | 1.9 | |
| lmo1433 | Glutathione reductase (NADPH) [Methanosarcina acetivorans] (4e-91) | TTTTTCGTTTGAAAGTGAAATCAGACGGGAAAACAAGCTAAG-N14-GTG | 6.8 | 5.7 | ||
| ctc | B. subtilis general stress protein Ctc (le-27) | TCCTTTGTTTTGCTATTTTTCTAAAGGGTAGATATAATGTA-N35-ATG | ctc (le-33)‡ | 1.5 | 2.2 | |
| lmo1602 | General stress protein [Oceanobacillus iheyensis] (6e-11) | AAGAAAGTTTTAGAGGGGAATACTCAGGGTATAGAAAAAGGA-N18-ATG | ytxG (6e-13)‡ | 2.7 | 2.1 | |
| Virulence and virulence associated | bsh | Bsh bile salt hydrolase (Lmo2067) | AATTATGTTTTACTCCAAACTCCGAGGGTACTGGTATACAT-N31-ATG | 10.8 | 20.1 | |
| inlA | Internalin A | CCATTAGTGTTATTTTGAACATAAAGGGTAGAGGATAACAT-N437-GTG† | 6.2 | 3.9 | ||
| inlB | Internalin B | CCTTTTGTTAGGGTTATTAGCAGTAGGAACTGCAATGGCTC-N113-GTG† | 4.6 | 2.1 | ||
| inlC2 | Internalin C2 | TTTTTTGTTAATTTGGTCTAAAAAAGGGTATCTATTATTAA-N55-ATG† | 11.4 | 7.3 | ||
| inlD | Internalin D | None found | 3.3 | 2.3 | ||
| inlE | Internalin E | TAAATCGTTAACAAGTCTAATTTTAGTGATTAAACGAAATC-N84-ATG† | 3.7 | 2.4 | ||
| Transporters | opuC operon | TAAAAAGTTTAAATCTATACTAGTTAGGGAAATTAGTTATCG-N48-GTG | ||||
| opuCA | Glycine betaine/carnitine/choline ABC transporter (ATP-binding protein) | opuCA (e-159) | 5.3 | 6.5 | ||
| opuCB | Glycine betaine/carnitine/choline ABC transporter (membrane protein) | opuCB (le-74) | 3.8 | 4.7 | ||
| opuCC | Glycine betaine/carnitine/choline ABC transporter (osmoprotectant-binding) | opuCC (le-92) | 4.1 | 5.2 | ||
| opuCD | Betaine/carnitine/choline ABC transporter (membrane protein) | opuCD (5e-66) | 5.0 | 5.8 | ||
| lmo0784 | PTS enzyme IIAB, mannose-specific [Yersinia pestis KIM] (5e-34) | AATTGCGTTTTCTGACTAATCTTTTAGGGTAATGTTGTATGT-N195-ATG | levD (le-21) | 7.5 | 5.0 | |
| lmo2602 | Cation-transporting ATPase [Oceanobacillus iheyensis] (2e-12) | TTGATTGTTTTGGTTTAATGCCAAAGGGAATATATTAACGT-N16-ATG | sapB (le-09) | 5.5 | 3.8 | |
| lmo0405 | PHO4, phosphate transporter family [Bacillus anthracis] (4e-76) | GATTCTTTTTATATTTGTATAAAAGGGGTATAGACAATAAA-N30-ATG | 3.9 | 4.9 | ||
| lmo2463 | Probable export protein (antibiotic) [Streptomyces coelicolor] (6e-80) | AATGATGTTTGGCATATGTAAAAAAGAGGTATAAATTAGCGTG | ydfJ (4e-30) | 3.0 | 5.2 | |
| lmo1539 | Glycerol uptake facilitator [Bacillus halodurans] (8e-66) | AAATGGGTTATAACTCTCGCGAATTGGGGTAAAAGTAAAGAG-N254-ATG | glpF (5e-81) | 2.4 | 2.3 | |
| lmo1421 | ABC transporter [Bacillus anthracis A2012] (8e-98) | AATTAGGAATATTTAGGGATGATTTAGGGTAATTGGATGATA-N74-ATG† | 2.5 | 2.1 | ||
| lmo0524 | Sulfate transporter [Mycobacterium tuberculosis CDC1551] (2e-50) | AGAGATGATTGTTCTATGTCAAAACGGGTAAATAGTATAAG-N65-ATG | 2.0 | 2.9 | ||
| lmo0593 | Formate/nitrite transporter family protein [Streptococcus agalactiae] (7e-37) | TTTTGTGTTTTAAGAGTTTGAAAACGGGGAAATTAACAACAT-N146-TTG | ywcJ (le-18) | 2.9 | 2.3 | |
| Metabolism | lmo0669 | Oxidoreductase [Oceanobacillus iheyensis] (3e-86) | TTAAACGTTTTAGCGTAAAACAGGAGGGAAGACATAAAGTA-N139-ATG | yhxD (3e-95)‡ | 14.2 | 9.5 |
| lmo1694 | Epimerase, NAD-dependent family [Bacillus anthracis] (2e-62) | AAAATGGTTTTAATACTACTAAAAAGGGAATAAACTAGTTA-N22-TTG | yfhF (5e-59)‡ | 11.5 | 11.7 | |
| lmo1883 | Chitinase [Serratia marcescens] (e-117) | TTTCTAGTTTTATTTTCACTATGTTGGGTATTTTCTAGTAG-N47-ATG | 4.1 | 2.1 | ||
| lmo2695 | Dihydroxyacetone kinase [Bacillus halodurans] (e-103) | AACCACGTTTTGACTTTCTAGTAAAGGGAAATTGAGGTAAG-N30-ATG | 2.8 | 4.3 | ||
| lmo0956 | N-Acetylglucosamine-6-phosphate deacetylase [Bacillus anthracis] (e-110) | TTTTTTGGTTATTTTACTTTTTTTCGGGTAAATAGGAAAAG-N71-ATG | nagA (le-72) | 1.8 | 1.4 | |
| lmo2205 | Phosphoglycerate mutase [Neisseria meningitidis] (4e-86) | AAAAAGGTTTGACACTTCACTTGAAAGGGAAAACTTTGGTTG-N44-ATG | 1.8 | 3.2 | ||
| pdhA | Pyruvate dehydrogenase (E1 alpha subunit) [Bacillus subtilis] (e-151) | ACCCATGTTTTCAATGAGGAATTTGTGGTAATAACTGGAGAG-N231-ATG | pdhA (e-162) | 1.7 | 1.6 | |
| lmo1933 | GTP cyclohydrolase I [Bacillus halodurans] (6e-67) | TTAGTGGTTTTCTGTTTTAGAAATAGGGAATATAATTACGA-N113-ATG | mtrA (7e-73)‡ | 2.0 | 2.0 | |
| Transcriptional regulation | rsbV operon | TTGAATGTTTTAATTTTATTTGTTAGGGTAAAATCGACAGT-N27-ATG† | ||||
| rsbV | Anti-anti-sigma factor (antagonist of RsbW) | rsbV (3e-24)‡ | 2.1 | 2.0 | ||
| rsbW | Sigma B activity negative regulator RsbW | rsbW (3e-42)‡ | 2.0 | 2.4 | ||
| sigB | RNA polymerase sigma-37 factor (sigma B) | sigB (7e-97)‡ | 2.2 | 2.3 | ||
| rsbX | Indirect negative regulation of sigma B (serine phosphatase) | rsbX (le-26)‡ | 2.0 | 2.2 | ||
| lmo2485 | Transcriptional regulator [Methanosarcina mazei Goel] (le-04) | GCAAAAGTAGGAAATGGAATTATCAAGGTTTCTGAACTCGA-N42-ATG | 1.8 | 3.9 | ||
| Cell wall | lmo2085 | Surface-anchored protein (LPXTG motif) [Listeria innocua] (le-18) | CTGGCTGTTTTCTTTTGCTGTTTTATGGGTATTTAATGATGT-N28-ATG | 14.7 | 10.7 | |
| lmo0880 | Surface-anchored protein (LPXTG motif) [Listeria innocua] (le-26) | TGTACGGTTTTTAACAAGCAAGTTGTGGGAACCTATAAAGATA-N26-ATG | 5.2 | 2.1 | ||
| Energy | qoxA | AA3-600 quinol oxidase subunit II | TTTTTTGTTTCGAATTTCACAATCTAGGGAATAGTGAACAGA-N265-GTG | qoxA (3e-91) | 1.5 | 1.9 |
| lmo2389 | Pyridine nucleotide-disulfide oxidoreductase [Bacillus anthracis] (e-123) | GATATAGTTTGTAAGCTGTGAAATAGGGAATATATTGGTAC-N127-ATG | yumB (e-128)‡ | 1.6 | 3.4 | |
| Translation | lmo1698 | Ribosomal protein (S5)-alanine N-acetyltransferase [Bacillus halodurans] (3e-) | TGGAAAGTTTATTTTTTAATAAAATGGGTATATAGAAAAAT-N72-ATG | yjcK (3e-55) | 3.1 | 1.9 |
| lmo2511 | Ribosomal_S30, sigma 54 modulation protein [Bacillus anthracis] (2e-53) | AAAGAGGTTTGCGGAAGCGGTATTAGTGGAATAAAATACTAA-N135-ATG | yvyD (e-162)‡ | 3.8 | 1.9 | |
| DNA translocase | lmo1606 | DNA translocase (spoIIIE) [Bacillus halodurans] (e-168) | TACCATGTTTAACCCCTCTATTACCAAGGTATTATAACGAAT-N97-ATG | ytpT (0.0) | 2.4 | 2.6 |
| Hypothetical | lmo2570 | Hypothetical protein YvaZ [Bacillus subtilis] (.023) | CAACAGGTGTTCTAGAATATTTACGGGAACAAAAAGTCGA-N234-ATG | yvaZ (5e-09) | 5.3 | 5.9 |
| lmo2269 | YhzC of Listria monocytogenes (9e-26) | TTTTAAGATTGTAATAAATATGAGTGAAGGAGTGGTAGTCGTG | 4.0 | 5.3 | ||
| lmo0911 | BH2119-unknown [Bacillus halodurans] (le-06) | CATCTTGTTTTAACTTGCCCTCAGGCGGGTATTTATTATATG-N53-ATG | 2.2 | 1.9 | ||
| lmo0794 | Conserved hypothetical protein YwnB [Bacillus subtilis] (2e-50) | ATAAATGTTTCCCAGTCCCCTCTTTCGGGAATAATTCTTCTA-N45-ATG | ywnB (5e-54) | 5.2 | 5.8 | |
| lmo1580 | Conserved hypothetical ATP-binding domain [Bacillus anthracis] (2e-40) | TTTTATGGTTCTTTTAGGAAAAAGAGGGTAAAATATAAGTA-N35-ATG | yxiE (4e-11) | 2.0 | 2.7 | |
| lmo2673 | Conserved hypothetical ATP-binding domain [Bacillus anthracis] (4e-28) | AATCATGCTTCTTTCTTTTATTTATGGGTATTAAGTAAATA-N30-ATG | 3.7 | 6.9 | ||
| lmo2386 | Conserved hypothetical protein YuiD [Bacillus subtilis] (le-37) | GAATAGGTTTTTAATAAGCTCATTGTGGTAAAATAAGAATAG-N22-ATG | yuiD (le-50) | 1.8 | 2.4 | |
| lmo2399 | Hemolysin homolog YhdP [Bacillus subtilis] (2e-89) | CTTGTGGTTTAAACGCTAAGAACGGGTATAGAATGGGGA-N15-ATG | 2.0 | 2.5 | ||
| lmo0438 | No similarity | ACTAACGAATCGCGTGGATGCGCTTCGGGAATTGTTGAAATA-N157-GTG | 2.7 | 3.4 | ||
| lmo0994 | No similarity | GAAAGAGGTTATTTTTCACTAAATGGGGTAAAAATACGTTA-N257-ATG | 6.1 | 6.5 | ||
a
The function of the protein encoded is listed if it has been supported by genetic or biochemical data. Otherwise, the nearest homologue of the protein with known function is listed. The E values in parentheses were obtained with Blast 2.0 searches with the BLOSUM62 matrix against the nr database. PTS, phosphotransferase system.
b
The promoter sequence as predicted by HMM is listed. For genes without an HMM-predicted promoter sequence (marked with †), a putative promoter identified by visual inspection is indicated; “none found” indicates that no suitable promoter could be found by HMM or visual inspection. The expected −35 and −10 regions are in bold, and the last nucleotide triplet is the presumed translational start codon.
c
The B. subtilis genome was searched for ORFs encoding proteins homologous to the given L. monocytogenes protein by Blast 2.0 on the SubtiList web server (http://genolist.pasteur.fr/SubtiList). The closest homologue is listed, if one was found, along with the E value in parentheses. Homologues that have been determined to be σB dependent in B. subtilis (51,53) are marked with ‡.
d
Change was calculated with SAM based on microarray data (see the text) and equals the average wild-type spot intensity divided by the average mutant spot intensity for two separate arrays from each of two replicate RNA isolations. Numbers in italics indicate ratios that were determined by SAM to not be statistically significantly different from a ratio of 1.0. ST, stationary-phase cells; OS, osmotically stressed cells (0.5 M KCl).