TABLE 2.
Defined ςB promoters of the control genes and promoters of the presumable new ςB-dependent genes found in this study
| Group and promoter sequencea | Gene | Protein
|
Presumed function and/or similarity | Probably cotranscribed gene(s) | |
|---|---|---|---|---|---|
| Molecular mass (kDa) | pI | ||||
| A (ςB-dependent genes [positive controls]) | |||||
| CGAGGTTTAAATCCTTATCGTTAT-GGGTATTGTTTGTAATAG-N33-ATG | ctc | 22.0 | 4.24 | Belongs to the L25P family of ribosomal proteins | |
| ACGTGTTTATTTTTTTGAAAAA---GGGTATGTAACTTG-TAC-N23-ATG | gspA | 33.5 | 5.19 | Similar to lipopolysaccharide-1,3-galactosyltransferases and to lipopolysaccharide-1,2-glucosyltransferases | |
| TCAGGTTTTAAAACAGCTCCGGCA-GGGCATGGTAAAGTACAT-N241-ATG | trxA | 11.39 | 4.34 | Thioredoxin | |
| B (genes controlled by ςB) | |||||
| ATTCGTTTACATATTGGCTTCAG--CGGAAATAGAAGAAGACA-N25-ATG | aldY | 52.8 | 5.07 | Probable aldehyde dehydrogenase, contains an aldehyde dehydrogenase signature (glutamic acid active site) | |
| AAGTGTTTCGAAATGATCAGGAGC-GGATATTGATTGGTAAAT-N21-ATG | ydaS | 8.64 | 12.22 | Membrane protein, unknown function | |
| ATGCGTTTTTATTTTTCACCTGC--GGGTACCATTTTTATAAA-N19-ATG | ydaT | 16.5 | 6.38 | Unknown | ydaS |
| GTTTGATTACAGCCAGAGCTGTCTGCAGGGAAACATTATGTTCTG-N193-ATG | ydbP | 12.4 | 4.42 | Similar to thioredoxins of A. fulgidus and S. cerevisiae | |
| TTATGTTTGGCTTTGCAAACAAAG-GGGAATAGGACAAACTGC-N76-TTG | ydhK | 22.5 | 7.81 | Protein with 1 transmembrane domain, unknown function | |
| ACATGTTTCACCAGCCTGTCAATCAGGGAATACCACTTATATC-N26-ATG | yfhK | 18.7 | 10.37 | Protein probably with signal sequence, similar to proteins with unknown function | |
| AAAGGTTTATGTTTTTCCATCTAT-GGGAAATGATTCATAAAC-N17-ATG | yflA | 50.6 | 10.4 | Integral membrane protein, similar to amino acid carrier protein | |
| TGGCGTTTATTCATTTCTGTCGTG-TGGTAACGTTCAGTATCA-N24-GTG | yhdF | 31.4 | 5.9 | Similar to glucose-1-dehydrogenase, belongs to the short-chain dehydrogenases/reductases family | |
| ACATGTTTCGTTGCAAAAACACG--GGGAAACGGAATGGTAGA-N19-ATG | yjgB | 20.8 | 6.68 | Membrane lipoprotein, unknown function | |
| AATGGTTTAATGATTTTCATGATGAGGGAATAATAAATGTATT-N25-ATG | ykgA | 29.6 | 4.88 | Function unknown, similar to streptococcal acid lipoprotein | ykgB |
| TCTAGTTTCTCTTTTTAAAAGAGTAGGGTATTGCAAACAACAG-N58-ATT | yotK | 7.2 | 7.69 | Unknown | |
| AACGGTGTTTTTTTATTTGATAG--GGGAAAATATAAAATGGA-N64-ATG | yoxA | 37.2 | 6.00 | Similar to hypothetical proteins of B. subtilis | pbp |
| TTCTGATTAAAAAAACGGATACA--GGGTAATGACATAAGAAA-N12-ATG | yoxC | 11.39 | 10.37 | Protein probably with signal or transmembrane sequence, similar to the general stress protein YtxG | yoxB, yoaA |
| TGCTGATTATACAAAAAGTGGATT-GGGAATGATAAAAGAACA-N21-ATG | ypuB | 7.23 | 4.24 | Protein with 1 transmembrane domain, unknown function | ypuC |
| TTCGGTTTTTCACCTGTCCAGAAACTGGGCTAGCTGGATTCGAAC-N136-ATG | yqhA | 31.8 | 5.17 | Membrane protein with 1 transmembrane domain, similar to RsbR of B. subtilis | |
| CTGCGAGTAAAATTTGAAAATAAC-GGGTATAATGCATGTAGG-N118-ATG | yqhQ | 36.0 | 9.71 | Integral membrane protein with unknown function | yqhP |
| ACTGGTTTAGTGACGCGGTTATT--GGGCAATTAAAGAATAAA-N25-ATG | yqxL | 37.7 | 10.00 | Membrane protein, similar to divalent cation transport proteins | |
| CCATGTTTAAAACCAGTCTTGATT-GGGAAAGTTACCTCAATA-N21-ATG | yrvD | 12.2 | 9.16 | Membrane protein with unknown function | yrvE, apt |
| ATAAGTTTTTCAGCTTTTTAAAAA-GGGAAAATAAAAAAAACA-N24-ATG | ytkL | 10.9 | 6.41 | Similar to proteins with unknown function | |
| AGTGGTTTGGACACCTCTTTGCC--GGGAATAACAATATATAG-N24-ATG | yvrE | 33.2 | 4.65 | Similar to the eukaryotic SMP-30/CGR1 protein family | |
| TTTTGTTTGAAAAAGAAAAGGGAC-AGGAAAAATAGGAAAAGA-N19-ATG | yxkO | 29.9 | 5.8 | Membrane protein with unknown function, similar to hypothetical family of uncharacterized proteins (UPF0031) | |
| GATCGTTTCGGACAGTAACAAGGC-GGGAAAAATGCAATAAAA-N19-ATG | yycD | 7.4 | 4.81 | Unknown | |
| C (complex-regulated genes, ςB could be involved) | |||||
| AATTGAATTGACCGGATCTTGGCC-TGGAAAACCAATGACTAA-N363-ATG | lctE | 34.9 | 5.64 | l-Lactate dehydrogenase | lctP |
| TTTCGGTTAAAACCTTATGAATAC-GGGTATATTAATGTTGGT-N74-ATG | yacL | 40.8 | 5.01 | Membrane protein, similar to hypothetical proteins | yacM, yacN, gltX |
| AACGGATTACTTTTGCTGACAGC--GGGAATTAACGGTAATAT-N153-ATG | ycnH | 50.2 | 4.8 | Similar to the succinate-semialdehyde dehydrogenase GabD of E. coli, contains an aldehyde dehydrogenase signature (cysteine active site) | |
| GGCTGTTTAAACAAGAAGAAAATG-GGGTATATCTAAAAGTAT-N30-ATG | yjbC | 23.1 | 5.22 | Unknown | yjbD |
| TTCGGAATTTATATTACAAAAT---GGATAAATATGGCCTTGC-N143-ATG | yqiS | 31.7 | 8.18 | Protein with 1 transmembrane domain, similar to phosphate butyryltransferases, belongs to the phosphate acetyltransferase and butyryltransferase family | yqiT, yqiV, yqiW, bfmBAA, bfmBAB, bfmBB |
| ATACGACTATTTCACTTGAAAATC-GGGTATATGTTTTTACAG-N83-ATG | ysdB | 15.6 | 9.85 | Membrane protein with unknown function | |
| D (noninducible genes preceded by a putative ςB promoter sequence) | |||||
| ATGAGTTTAACGCAAATGTGGC---GGGAATCGGCGTCTTAGT-N157-ATG | yabJ | 13.6 | 5.24 | Unknown, similar to proteins with unknown function | |
| AAAGGTTTATTTGGGGATGGCG---GGGAATGTATAGGAGAAA-N34-ATG | yhaR | 29.5 | 6.27 | Protein with 1 transmembrane domain, similar to 3-hydroxybutyryl-coenzyme A-dehydratase | yhaQ, yhaP |
| AGGTGTGTGAAAATATTCGGTAATAGGGTAAAAAAACCTTGAT-N86-ATG | yqhZ | 14.8 | 4.8 | Unknown, similar to NusB (transcription termination) | folD |
a
Boldface sequences represent, from left to right, −35 region, −10 region, and transcriptional start site (+1). Start codons are indicated on the far right.