TABLE 2.
Genes upregulated by σB
| N315 ORF no.a | N315 genea | N315 descriptiona | Fold changeb in strain:
|
σB consensusc,d | Reference(s) with reported σB dependencee for:
|
|||
|---|---|---|---|---|---|---|---|---|
| COL | Newman | GP268 | S. aureus | B. subtilisf | ||||
| N315-SA1984 | asp23 | Alkaline shock protein 23 | Up | Up | Up | Yes | 24, 26, 44, 55 | |
| CAB75732.1 | bbp | Bone sialoprotein-binding protein Bbp | 3.2 | 4.5 | 4.8 | ? | — | |
| N315-SA2008 | budB | α-acetolactate synthase | Up | Up | Up | Yesd | ||
| N315-SA0144 | cap5A | Capsular polysaccharide synthesis enzyme Cap5A | Up | Up | 12.8 | ? | ||
| N315-SA0145 | cap5B | Capsular polysaccharide synthesis enzyme Cap5B | Up | Up | 10.8 | ? | ||
| N315-SA0146 | cap5C | Capsular polysaccharide synthesis enzyme Cap8C | Up | Up | 8.6 | ? | ||
| N315-SA0147 | cap5D | Capsular polysaccharide synthesis enzyme Cap5D | Up | Up | 7.3 | ? | ||
| N315-SA0148 | cap5E | Capsular polysaccharide synthesis enzyme Cap8E | Up | Up | 7.5 | ? | ||
| N315-SA0149 | cap5F | Capsular polysaccharide synthesis enzyme Cap5F | Up | Up | 7.5 | ? | ||
| N315-SA0150 | cap5G | Capsular polysaccharide synthesis enzyme Cap5G | Up | Up | 6.8 | ? | ||
| N315-SA0151 | cap5H | Capsular polysaccharide synthesis enzyme Cap5H | Up | Up | 5.1 | ? | — | |
| N315-SA0152 | cap5I | Capsular polysaccharide synthesis enzyme Cap5I | Up | Up | 5.7 | ? | — | |
| N315-SA0153 | cap5J | Capsular polysaccharide synthesis enzyme Cap5J | Up | Up | 3.5 | ? | — | |
| N315-SA0155 | cap5L | Capsular polysaccharide synthesis enzyme Cap5L | Up | Up | 5.1 | ? | ||
| N315-SA0156 | cap5M | Capsular polysaccharide synthesis enzyme Cap5M | Up | Up | 4.5 | ? | ||
| N315-SA0157 | cap5N | Capsular polysaccharide synthesis enzyme Cap5N | 2.7 | Up | 5.2 | ? | ||
| N315-SA0158 | cap5O | Capsular polysaccharide synthesis enzyme Cap8O | 2.6 | Up | 4.2 | ? | ||
| CAA79304 | clfA | Clumping factor A | 35.7 | Up | 7.8 | Yes | 33, 60 | |
| N315-SA2336 | clpL | ATP-dependent Clp proteinase chain ClpL | 17.3 | 13.2 | Up | Yes | 25, 33 | |
| N315-SA2349 | crtM | Squalene desaturase | Up | Up | Up | Yesd | 26 | 66 (yisP) |
| N315-SA2348 | crtN | Squalene synthase | Up | Up | Up | Yesd | 26 | |
| N315-SA1452 | csbD | HP, σB-controlled gene product CsbD (Csb8) | 37.0 | Up | Up | Yes | 25, 33 | 30, 66 (ywmG) |
| COL-SA1872 | epiE | Epidermin immunity protein EpiE | Up | Up | Up | Yesd | — | |
| COL-SA1873 | epiF | Epidermin immunity protein EpiF | Up | Up | Up | Yes | — | |
| N315-SA1634 | epiG | Epidermin immunity protein EpiG | Up | Up | Up | Yesd | — | |
| N315-SA2260 | fabG | HP, similar to glucose l-dehydrogenase | Up | Up | Up | Yes | 30 (yxbG) | |
| N315-SA1901 | fabZ | (3R)-hydroxymyristoyl-[acyl carrier protein] dehydratase | 2.2 | 5.1 | 2.0 | Yesd | ||
| N315-SA2125 | hutG | HP, similar to formiminoglutamase | 3.7 | 14.6 | 2.9 | Yes | ||
| N315-SA1505 | lysP | Lysine-specific permease | 2.4 | 7.9 | 2.0 | ? | ||
| N315-SA1962 | mtlA | PTS system, mannitol-specific IIA component | 8.5 | 17.2 | Up | Yesd | ||
| N315-SA1963 | mtlD | Mannitol-l-phosphate 5-dehydrogenase | 8.2 | Up | Up | Yesd | ||
| N315-SA1902 | murA | UDP-N-acetylglucosamine l-carboxyvinyl transferase 1 | 2.2 | 5.1 | 2.0 | Yesd | ||
| N315-SA0547 | mvaK1 | Mevalonate kinase | 2.4 | 4.5 | 1.3 | Yes | ||
| N315-SA0548 | mvaD | Mevalonate diphosphate decarboxylase | 3.3 | 7.3 | 1.8 | Yesd | — | |
| N315-SA0549 | mvaK2 | Phosphomevalonate kinase | 3.7 | 10.6 | 2.2 | Yesd | ||
| N315-SA1987 | opuD | Glycine betaine transporter opuD homologue | Up | Up | Up | Yes | 26, 33 | |
| N315-SA1871 | rsbV | Anti-σB factor antagonist | Up | Up | Up | Yes | 26, 43, 82 | 30, 66 |
| N315-SA1870 | rsbW | Anti-σB factor | Up | Up | Up | Yesd | 26, 43, 82 | 30, 66 |
| N315-SA0573 | sarA | Staphylococcal accessory regulator A (Csb35) | 2.9 | 3.8 | 2.0 | Yes | 4, 15, 25, 55 | |
| N315-SA0108 | sarS | Staphylococcal accessory regulator A homologue S | 2.6 | 1.1 | 2.1 | Yes | 77 | — |
| N315-SA0099 | sbtA | HP, similar to transmembrane efflux pump protein | Up | Up | Up | ? | 66 (yusP) | |
| N315-SA1869 | sigB | Alternative transcription factor σB | Up | Up | Up | Yesd | 26, 43, 82 | 30, 66 |
| N315-SA0456 | spoVG | Stage V sporulation protein G homologue | 4.3 | 9.8 | 3.0 | Yesd | ||
| N315-SA1114 | truB | tRNA pseudouridine 5S synthase | 2.1 | Up | 2.3 | Yes | ||
| N315-SA2119 | ydaD | HP, similar to dehydrogenase (Csb28) | 4.8 | 33.1 | 16.9 | Yes | 25 | 30 (yhxD) |
| N315-SA0084 | HP, similar to Homo sapiens CG1-44 protein | Up | Up | 3.0 | Yes | — | ||
| N315-SA0098 | HP, similar to aminoacylase | Up | Up | Up | ? | |||
| N315-SA0102 | 67 kDa myosin-crossreactive streptococcal antigen homologue | Up | Up | Up | Yes | — | ||
| N315-SA0105 | HP | Up | Up | Up | ? | — | ||
| N315-SA0163 | HP, similar to cation efflux system membrane protein CzcD | Up | Up | Up | ? | |||
| N315-SA0164 | HP | Up | Up | Up | Yes | — | ||
| N315-SA0261 | HP, similar to rbs operon repressor RbsR | 2.5 | Up | Up | Yes | |||
| N315-SA0296 | Conserved HP | 7.6 | 20.5 | 3.9 | Yes | — | ||
| N315-SA0297 | HP, similar to ABC transporter ATP-binding protein | 6.3 | 13.1 | 2.8 | Yesd | — | ||
| N315-SA0317 | HP, similar to dihydroflavonol-4-reductase | 11.6 | 20.7 | 3.9 | Yes | — | ||
| N315-SA0326 | Conserved HP | 2.5 | 2.1 | 2.0 | Yes | |||
| N315-SA0327 | Conserved HP | 2.2 | 2.1 | 2.0 | Yesd | — | ||
| N315-SA0359 | Conserved HP | Up | Up | Up | Yes | 33 | ||
| N315-SA0360 | Conserved HP | Up | Up | 77.7 | Yes | 30, 66 (ydaS) | ||
| N315-SA0372 | HP (Csb12) | 1.6 | 3.3 | 2.0 | Yes | 25 | — | |
| N315-SA0455 | Translation initiation inhibitor homologue | 3.2 | 6.2 | 2.3 | Yes | 33 | ||
| N315-SA0509 | Conserved HP | 2.0 | 12.1 | 2.0 | ? | — | ||
| N315-SA0528 | HP, similar to hexulose-6-phosphate synthase (Csb4) | 1.8 | 6.8 | 2.0 | Yes | 25 | ||
| N315-SA0529 | Conserved HP (Csb4-1) | 1.9 | 8.7 | 2.0 | Yesd | 25 | ||
| N315-SA0541 | HP, similar to cationic amino acid transporter | 11.3 | 14.4 | 7.7 | Yes | 30 (yhdG) | ||
| N315-SA0572 | HP, similar to esterase/lipase | Up | Up | Up | Yes | |||
| N315-SA0577 | HP, similar to FimE recombinase | Up | Up | Up | ? | |||
| N315-SA0578 | HP, similar to NADH dehydrogenase | Up | Up | Up | Yes | |||
| N315-SA0579 | HP, similar to Na+ H+ antiporter | Up | Up | 4.0 | Yesd | |||
| N315-SA0580 | HP, similar to Na+ H+ antiporter | Up | Up | Up | Yesd | |||
| N315-SA0581 | MnhD homologue, similar to Na+ H+ antiporter subunit | Up | Up | 6.0 | Yesd | |||
| N315-SA0582 | HP, similar to Na+ H+ antiporter | Up | Up | 4.0 | Yesd | |||
| N315-SA0583 | HP, similar to Na+ H+ antiporter | Up | Up | 4.7 | Yesd | |||
| N315-SA0584 | Conserved HP | Up | Up | 5.3 | Yesd | |||
| N315-SA0633 | HP | 2.0 | 8.7 | 2.9 | Yesd | 33 | — | |
| N315-SA0634 | Conserved HP | 1.9 | 6.6 | 2.3 | Yesd | |||
| N315-SA0635 | Conserved HP | 5.1 | 14.8 | 2.8 | Yesd | |||
| N315-SA0636 | Conserved HP | 5.5 | 22.9 | 2.2 | Yesd | |||
| N315-SA0637 | Conserved HP | 5.3 | 24.3 | 3.5 | Yes | — | ||
| N315-SA0658 | HP, similar to plant metabolite dehydrogenases | 3.0 | 10.5 | 2.5 | Yes | — | ||
| N315-SA0659 | HP, similar to CsbB stress response protein | 3.3 | 10.4 | 2.5 | Yesd | 30, 66 (csbB) | ||
| N315-SA0665 | Coenzyme PQQ synthesis homologue | 2.1 | 4.5 | 1.8 | ? | |||
| N315-SA0666 | 6-Pyruvoyl tetrahydrobiopterin synthase homologue | 2.3 | 5.7 | 2.1 | ? | |||
| N315-SA0681 | HP, similar to multidrug resistance protein (Csb29) | 2.4 | Up | Up | Yes | 25 | 30, 66 (bmrU) | |
| N315-SA0721 | Conserved HP | 4.2 | 10.3 | 2.4 | Yes | |||
| N315-SA0722 | Conserved HP | 3.4 | 9.4 | 1.5 | Yesd | |||
| N315-SA0724 | HP, similar to cell division inhibitor | 2.5 | 3.8 | 2.5 | Yes | 30, 66 (yfhF) | ||
| N315-SA0725 | Conserved HP | Up | Up | Up | ? | — | ||
| N315-SA0740 | HP | Up | Up | Up | Yes | — | ||
| N315-SA0741 | Conserved HP | Up | Up | Up | Yesd | — | ||
| N315-SA0748 | HP | 3.0 | Up | 4.8 | Yesd | — | ||
| N315-SA0749 | HP | 2.5 | Up | 6.6 | Yes | — | ||
| N315-SA0751 | HP | 4.3 | 5.7 | 4.1 | ? | — | ||
| N315-SA0752 | HP | Up | Up | Up | Yes | 33 | — | |
| N315-SA0755 | HP, similar to general stress protein 170 | Up | Up | Up | Yes | 30, 66 (ykzA) | ||
| N315-SA0768 | Conserved HP | 2.0 | 5.6 | 4.5 | ? | |||
| N315-SA0772 | Conserved HP | Up | Up | Up | Yes | 33 | 30, 66 (csbD) | |
| N315-SA0774 | HP, similar to ABC transporter ATP-binding protein homologue (Csb10) | 2.1 | 2.0 | 1.4 | Yes | 25 | ||
| N315-SA0780 | HP, similar to hemolysin | 3.3 | Up | 2.2 | Yes | 30, 66 (yqhB) | ||
| N315-SA0781 | HP, similar to 2-nitropropane dioxygenase | 2.2 | Up | 2.0 | Yesd | |||
| N315-SA0933 | HP | 13.1 | 26.9 | 7.1 | Yes | — | ||
| N315-SA1014 | Conserved HP | Up | Up | Up | Yes | |||
| N315-SA1057 | Conserved HP | 2.4 | 3.9 | 3.1 | Yes | |||
| N315-SA1559 | HP, similar to smooth muscle caldesmon | 3.6 | 12.1 | 2.1 | Yesd | — | ||
| N315-SA1560 | HP, similar to general stress protein homolog | 2.8 | 8.2 | 2.2 | Yes | 30, 66 (ytxG) | ||
| N315-SA1573 | HP | 5.9 | 21.0 | 3.0 | Yes | — | ||
| N315-SA1590 | HP | 2.0 | 4.3 | 2.1 | Yes | — | ||
| N315-SA1657 | Conserved HP | 2.0 | 4.5 | 2.4 | Yes | |||
| N315-SA1671 | HP (Csb33) | 3.0 | 9.4 | 2.1 | Yes | 25 | — | |
| N315-SA1692 | Conserved HP (Csb3) | 1.8 | 5.6 | 4.0 | ? | 25 | ||
| N315-SA1697 | HP, similar to protein-tyrosine phosphatase | 2.3 | 5.0 | 3.7 | Yes | 30 (yfkJ) | ||
| N315-SA1698 | HP | 1.3 | 2.9 | 2.0 | Yesd | — | ||
| N315-SA1699 | HP, similar to transporter | 5.0 | 23.1 | 6.1 | Yesd | 30, 66 (yfkH) | ||
| N315-SA1814 | HP, similar to succinyl-diaminopimelate desuccinylase | Up | Up | Up | ? | |||
| N315-SA1903 | Conserved HP | 3.7 | 10.9 | 3.7 | Yesd | |||
| N315-SA1924 | HP, similar to aldehyde dehydrogenase (Csb24) | 3.7 | 26.1 | 3.2 | Yes | 25 | ||
| N315-SA1942 | Conserved HP | 2.3 | 7.9 | 3.6 | ? | |||
| N315-SA1946 | Conserved HP (Csb9) | Up | Up | Up | Yes | 25, 33 | ||
| N315-SA1961 | HP, similar to transcription AT BglG family | 9.7 | 8.2 | Up | Yesd | |||
| N315-SA1980 | Conserved HP | 3.4 | 4.7 | 1.1 | Yesd | — | ||
| N315-SA1981 | Conserved HP | 5.7 | 7.7 | 1.6 | Yes | — | ||
| N315-SA1985 | HP | Up | Up | Up | Yesd | 26 | — | |
| N315-SA1986 | HP | Up | Up | Up | Yes | 26 | — | |
| N315-SA2006 | HP, similar to MHC class II analog | Up | Up | Up | ? | — | ||
| N315-SA2101 | Conserved HP | 2.2 | 3.3 | 1.5 | Yesd | 66 (yrhD) | ||
| N315-SA2102 | Conserved HP | 2.2 | 3.3 | 1.7 | Yes | |||
| N315-SA2104 | HP, similar to suppressor protein SuhB | 2.1 | 2.2 | 1.8 | Yes | |||
| N315-SA2158 | HP, similar to TpgX protein | 2.2 | 3.5 | 2.5 | Yes | |||
| N315-SA2203 | HP, similar to multidrug resistance protein | 2.1 | 3.9 | 2.2 | Yes | |||
| N315-SA2219 | Conserved HP | Up | Up | 3.0 | Yes | 33 | ||
| N315-SA2240 | HP, similar to para-nitrobenzyl esterase chain A | 1.9 | 2.0 | 2.0 | ? | |||
| N315-SA2242 | Conserved HP | Up | Up | Up | ? | |||
| N315-SA2243 | HP, similar to ABC transporter (ATP-binding protein) | Up | Up | Up | ? | |||
| N315-SA2262 | Conserved HP (Csb7) | Up | Up | Up | Yes | 25 | ||
| N315-SA2267 | HP | 3.0 | Up | 3.9 | Yes | — | ||
| N315-SA2298 | Conserved HP | 3.4 | 30.9 | 6.1 | ? | 33 | 30, 66 (ydhT) | |
| N315-SA2309 | Conserved HP | 2.0 | 2.5 | 2.9 | — | |||
| N315-SA2327 | HP, similar to pyruvate oxidase | 51.1 | Up | 17.9 | ? | 30, 66 (ydhP) | ||
| N315-SA2328 | Conserved HP | Up | Up | Up | ? | 66 (yxaC) | ||
| N315-SA2350 | Conserved HP | Up | Up | Up | Yesd | — | ||
| N315-SA2351 | HP, similar to phytoene dehydrogenase | Up | Up | Up | Yesd | — | ||
| N315-SA2352 | HP | Up | Up | Up | Yes | — | ||
| N315-SA2366 | Conserved HP | 7.3 | Up | 4.5 | Yes | — | ||
| N315-SA2367 | Conserved HP | 10.4 | Up | 8.9 | Yes | |||
| N315-SA2374 | Conserved HP | Up | Up | Up | ? | — | ||
| N315-SA2398 | HP | Up | Up | Up | Yes | — | ||
| N315-SA2403 | Conserved HP | 10.3 | Up | 8.7 | Yes | |||
| N315-SA2440 | HP | 2.3 | 5.9 | 1.7 | ? | — | ||
| N315-SA2441 | HP, similar to lipopolysaccharide biosynthesis protein | 2.5 | 6.6 | 2.0 | ? | |||
| N315-SA2442 | Preprotein translocase SecA homologue | 3.5 | 8.5 | 2.0 | ? | |||
| N315-SA2451 | HP | Up | Up | Up | Yes | 33 | — | |
| N315-SA2452 | Conserved HP | Up | Up | 3.5 | ? | |||
| N315-SA2479 | Conserved HP | Up | 4.3 | 4.6 | Yes | — | ||
| N315-SA2485 | HP | Up | Up | Up | Yes | — | ||
| N315-SA2488 | HP | Up | Up | Up | Yes | — | ||
| N315-SA2489 | HP, similar to high-affinity nickel-transport protein | Up | Up | Up | Yesd | — | ||
| N315-SA2491 | Conserved HP | Up | Up | Up | Yes | — | ||
| N315-SAS023 | HP, similar to thioredoxin | 2.1 | 4.6 | 3.2 | ? | — | ||
| N315-SAS049 | HP | Up | Up | Up | Yesd | — | ||
| N315-SAS053 | HP | 4.0 | 12.8 | 2.1 | Yesd | — | ||
| N315-SAS056 | HP | 2.0 | 5.7 | 1.9 | Yes | — | ||
| N315-SAS068 | HP | 5.2 | 5.7 | 3.3 | Yes | — | ||
| N315-SAS082 | HP | Up | Up | Up | ? | — | ||
| N315-SAS083 | HP | Up | Up | Up | ? | — | ||
| N315-SAS089 | HP | 2.6 | 5.7 | 2.3 | ? | — | ||
| COL-SA0866 | HP | Up | Up | Up | ? | — | ||
| COL-SA1046 | HP | 6.6 | 12.0 | 9.0 | Yes | — | ||
| COL-SA2012 | HP, acetyltransferase (GNAT) family | 5.8 | 2.9 | 2.0 | ? | — | ||
| COL-SA2013 | HP | Up | Up | Up | ? | — | ||
| COL-SA2379 | Conserved HP | 2.2 | 17.1 | 3.0 | ? | — | ||
| COL-SA2433 | HP | 2.6 | 3.6 | 2.1 | Yesd | — | ||
| COL-SA2481 | HP | Up | Up | Up | Yesd | — | ||
| COL-SA2595 | HP | 2.3 | 4.1 | 2.1 | ? | — | ||
| COL-SA2631 | Conserved HP | Up | Up | 3.8 | Yes | — | ||
| AAB05395 | HP, ORF 3 of the sarA locus | 11.8 | 46.6 | 6.8 | Yes | 4, 15, 52, 55 | — | |
| CAB60754 | HP | 32.1 | Up | 13.9 | Yes | — | ||
a
Based on the published sequence of strain N315 (accession no. NC_002745). For genes not present in N315, the gene name and description given are from the COL genome, available from The Institute for Genomic Research Comprehensive Microbial Resource website (http://www.tigr.org), or the respective accession number. ABC, ATP binding cassette; GNAT, GCN5-related N-acetyltransferases; HP, hypothetical protein; MHC, major histocompatibility complex; PTS, phosphotransferase system.
b
Normalized values in the rsbU+V+W+ sigB+ strain over values in the ΔrsbUVW-sigB mutant. “Up” denotes genes highly downregulated in the ΔrsbUVWsigB mutant, such that the transcripts were below detectable levels and the change could not be accurately calculated.
c
ORFs preceded by a consensus sequence that resembles the σB consensus sequence for B. subtilis as described by Petersohn et al. (64). Only sequences deviating not more than three nucleotides from the consensus GttTww12-15 gGgwAw (w = a, t) sequence and lying within 500 bp upstream of predicted ORFs were considered σB-dependent promoters. ?, genes or operons are not preceded by a σB consensus promoter that matches the criteria given above.
d
ORFs likely to form an operon.
e
References reporting an influence of σB on the respective gene or its gene product in S. aureus or the homologues gene in B. subtilis.
f
B. subtilis gene names are given in parentheses, if different from those of S. aureus. The absence of a homologous ORF in the B. subtilis genome is indicated by a dash.