TABLE 2.
E. coli genes whose relative expression levels were increased or decreased by baeR amplification
| Genea | b no.b | Known or predicted functionc | Effect of BaeR on gene expression (fold change)
|
|
|---|---|---|---|---|
| Microarray | Real-time PCR | |||
| Increased expression | ||||
| creD | b4400 | Tolerance to colicin E2 | 180 | 35,000 |
| spy | b1743 | Periplasmic protein related to spheroblast formation | 140 | 640 |
| mdtA (yegM) | b2074 | Membrane protein inolved in drug resistance | 140 | 490 |
| mdtB (yegN) | b2075 | Multidrug transport protein (RND family) | 24 | 280 |
| baeR | b2079 | Response regulator in two-component regulatory system with BaeS | 24 | 15,000 |
| malE | b4034 | Maltose transport protein, chemotaxis (ABC superfamily) | 22 | 37 |
| amn | b1982 | AMP nucleosidase | 22 | 21 |
| yiaD | b3552 | Putative outer membrane protein | 20 | 79 |
| ansB | b2957 | Periplasmic l-asparaginase II | 19 | 76 |
| yeeN | b1983 | Conserved protein | 15 | 17 |
| malK | b4035 | Maltose transport protein (ABC superfamily) (N terminal): phenotypic repressor of mal operon (C terminal) | 14 | 73 |
| garP (yhaU) | b3127 | Putative (d)-glucarate/galactarate transport protein (MFS family) | 13 | 86 |
| gsp | b2988 | Glutathionylspermidine amidase (N terminal); glutathionylspermidine synthetase (C terminal) | 13 | 29 |
| malM | b4037 | Periplasmic protein of mal regulon | 12 | 35 |
| lamB | b4036 | Maltoporin, high-affinity receptor for maltose and maltose oligosaccharides | 12 | 26 |
| yfjB | b2615 | NAD kinase | 10 | 18 |
| yieI | b3716 | Putative membrane protein | 9.3 | 50 |
| mdtC (yegO) | b2076 | Multidrug transport protein (RND family) | 9.1 | 190 |
| tsr | b4355 | Methyl-accepting chemotaxis protein 1, serine sensor receptor | 8.9 | 14 |
| baeS | b2078 | Sensory histidine kinase in two-component regulatory system wtih BaeR | 8.0 | 120 |
| tolC | b3035 | Outer membrane channel; tolerance to colicin E1 | 7.9 | 12 |
| yieJ | b3717 | Conserved hypothetical protein | 7.8 | 48 |
| phoB | b0399 | Response regulator in two-component regulatory system with PhoR (or CreC) | 7.8 | 18 |
| elaA | b2267 | Putative transferase | 7.3 | 15 |
| yghU | b2989 | Putative S-transferase | 7.2 | 14 |
| cheM (tar) | b1886 | Methyl-accepting chemotaxis protein II, aspartate sensor receptor | 7.1 | 6.3 |
| fliC | b1923 | Flagellar biosynthesis | 6.6 | 6.4 |
| garD (yhaG) | b3128 | (d)-Galactarate dehydrogenase | 6.5 | 18 |
| tap | b1885 | Methyl-accepting chemotaxis protein IV, peptide sensor receptor | 6.0 | 7.4 |
| garL (yhaF) | b3126 | Alpha-dehydro-beta-deoxy-d-glucarate aldolase | 6.0 | 32 |
| cheR | b1884 | Glutamate methyltransferase, chemotactic response regulator | 5.8 | 9.1 |
| yidS | b3690 | Putative oxidoreductase with FAD/NAD(P)-binding domaind | 5.7 | 130 |
| ypfH | b2473 | Conserved protein | 5.6 | 9.1 |
| phnD | b4105 | Phosphonate transport protein (ABC superfamily, peri_bind) | 5.6 | 140 |
| malF | b4033 | Maltose transport protein (ABC superfamily, membrane) | 5.5 | 28 |
| sulA | b0958 | Suppressor of lon; inhibitor of cell division and FtsZ ring formation upon DNA damage or inhibition | 5.4 | 5.2 |
| aroF | b2601 | 3-Deoxy-d-arabinoheptulosonate-7-phosphate synthase (DAHP synthetase), tyrosine repressible | 5.4 | 9.5 |
| flgL | b1083 | Flagellar biosynthesis; hook-filament junction protein | 5.4 | 5.9 |
| malG | b4032 | Maltose transport protein (ABC superfamily, membrane) | 5.3 | 19 |
| fliD | b1924 | Flagellar biosynthesis; filament capping protein; enables filament assembly | 5.3 | 8.1 |
| glpF | b3927 | MIP channel, glycerol diffusion | 5.2 | 10 |
| fliT | b1926 | Flagellar biosynthesis; putative export chaperone for FliD | 5.0 | 13 |
| phnJ | b4098 | Conserved protein in phn operon | 5.0 | 60 |
| ycaC | b0897 | Putative cysteine hydrolase | 5.0 | 7.3 |
| cheA | b1888 | Chemotactic sensory histidine kinase (soluble) in two-component regulatory system with CheB and CheY | 5.0 | 8.1 |
| icdA | b1136 | e14 prophage; isocitrate dehydrogenase, specific for NADP+ | 4.9 | 31 |
| phoR | b0400 | Sensory histidine kinase in two-component regulatory system with PhoB | 4.9 | 15 |
| flxA | b1566 | Qin prophage | 4.7 | 7.7 |
| fliS | b1925 | Flagellar biosynthesis; repressor of class 3a and 3b operons (RflA activity) | 4.7 | 6.2 |
| motB | b1889 | Enables flagellar motor rotation, linking torque machinery to cell wall | 4.5 | 6.4 |
| b1141 | b1141 | e14 prophage; putative exisionase | 4.5 | 19 |
| motA | b1890 | Proton conductor component of motor, torque generator | 4.4 | 6.6 |
| agaZ | b3132 | Tagatoso-6-phosphate aldolase I, subunit together with AgaY | 4.4 | 23 |
| cheW | b1887 | Purine-binding chemotaxis protein; regulation | 4.3 | 6.9 |
| cheZ | b1881 | Chemotactic response, CheY protein phophatase | 4.1 | 39 |
| ybiC | b0801 | Putative dehydrogenase | 4.1 | 8.2 |
| tsx | b0411 | Nucleoside channel; receptor of phage T6 and colicin K | 4.1 | 5.8 |
| acrD | b2470 | Aminoglycoside/multidrug efflux pump (RND family) | 4.1 | 35 |
| mdtD (yegB) | b2077 | Putative multidrug transport protein (MFS family) | 4.0 | 110 |
| Decreased expression | ||||
| ibpB | b3686 | Small heat shock protein | 0.25 | 0.17 |
| ibpA | b3687 | Small heat shock protein | 0.21 | 0.16 |