TABLE 2.
Genes showing transient repression upon cold shock in the wild-type strain
| Gene name and role | Gene product and/or function | 15°C/37°C ratio at 1 h | 15°C/37°C ratio at 5 h |
|---|---|---|---|
| Genes involved in membrane synthesis/function | |||
| fecA | Iron(III) dicitrate transport protein FecA precursor | 0.02 ± 0.005 | 0.22 ± 0.001 |
| fecB | Iron(III) dicitrate-binding periplasmic protein precursor | 0.04 ± 0.01 | 0.3 ± 0.08 |
| fecC | FecC protein | 0.02 ± 0 | 0.9 ± 0.2 |
| fecE | Membrane-bound iron (III) dicitrate transport protein | 0.01 ± 0.005 | 0.9 ± 0.07 |
| fepC | Ferric enterobactin transport protein FepC | 0.14 ± 0.03 | 0.7 ± 0.06 |
| fimD | FimD protein | 0.29 ± 0.04 | 1.9 ± 0.13 |
| kgtP | Alpha-ketoglutarate permease | 0.3 ± 0.02 | 0.45 ± 0.01 |
| lgt | Prolipoprotein diacylglyceryl transferase | 0.25 ± 0.005 | 0.54 ± 0.12 |
| lolA | Outer membrane lipoproteins carrier protein precursor | 0.27 ± 0.005 | 0.6 ± 0.04 |
| msbA | MsbA protein | 0.26 ± 0.015 | 0.6 ± 0.02 |
| nlpD | Lipoprotein D precursor | 0.7 ± 0.02 | 0.26 ± 0.02 |
| oppB | Oligopeptide transport system permease protein | 0.31 ± 0 | 1.1 ± 0.1 |
| oppC | Oligopeptide permease membrane protein | 0.27 ± 0.01 | 1.5 ± 0.2 |
| plsX | PlsX protein | 0.16 ± 0.03 | 1 ± 0.005 |
| potA | Spermidine/putrescine transport protein A | 0.22 ± 0.01 | 0.45 ± 0.08 |
| potB | Spermidine/putrescine transport system permease protein PotB | 0.12 ± 0.01 | 0.31 ± 0.045 |
| potC | Spermidine/putrescine transport system permease protein PotC | 0.19 ± 0.025 | 0.31 ± 0.015 |
| proP | Proline/betaine transport protein | 0.17 ± 0.01 | 0.48 ± 0.01 |
| proV | Glycine betaine/I-proline transport ATP-binding protein ProV | 0.01 ± 0.005 | 0.06 ± 0.005 |
| proW | Glycine betaine/proline transport system protein prow | 0.04 ± 0 | 0.07 ± 0.015 |
| proX | Glycine betaine-binding periplasmic protein precursor | 0.08 ± 0.01 | 0.11 ± 0.01 |
| secG | P12 cytoplasmic membrane protein | 0.3 ± 0.005 | 0.57 ± 0.05 |
| tolA | TolA protein | 0.29 ± 0.025 | 1.2 ± 0.2 |
| trkH | TrkH protein | 0.33 ± 0 | 1.3 ± 0.2 |
| wzxE | Lipopolysaccharide biosynthesis protein | 0.19 ± 0 | 0.88 ± 0.03 |
| Genes involved in cell metabolism | |||
| aceB | Malate synthase A (Msa) | 0.04 ± 0 | 0.1 ± 0.005 |
| adhC | Formaldehyde dehydrogenase (glutathione) | 0.26 ± 0.035 | 0.45 ± 0.045 |
| argB | Acetylglutamate kinase | 0.18 ± 0.01 | 0.75 ± 0.01 |
| argC | N-acetyl-gamma-glutamyl-phosphate reductase | 0.12 ± 0.04 | 3 ± 0.4 |
| argD | Acetylomithine aminotransferase | 0.14 ± 0.02 | 0.3 ± 0.1 |
| argG | Argininosuccinate synthase | 0.15 ± 0.04 | 1.3 ± 0.15 |
| argH | Argininosuccinate lyase | 0.25 ± 0.08 | 0.4 ± 0.05 |
| aroA | 3-Phosphoshikimate 1-carboxyvinyltransferase | 0.2 ± 0.01 | 0.45 ± 0.07 |
| aroB | 3-Dehydroquinate synthase | 0.3 ± 0.015 | 1.2 ± 0.24 |
| cmk | Cytidylate kinase (cytidine monophosphate kinase) | 0.24 ± 0.02 | 0.4 ± 0.01 |
| ddg | Ddg protein | 0.1 ± 0.01 | 1.4 ± 0.01 |
| fdhE | FdhE protein | 0.27 ± 0 | 0.7 ± 0.6 |
| folP | Dihydropteroate synthase | 0.29 ± 0.03 | 0.5 ± 0.02 |
| glcF | Glycolate oxidase iron-sulfur subunit | 0.07 ± 0.005 | 1.7 ± 0.27 |
| gltB | Glutamate synthase (NADPH) large chain precursor | 0.12 ± 0.02 | 0.5 ± 0.005 |
| hisF | Cyclase HisF | 0.3 ± 0.02 | 0.8 ± 0.2 |
| iclR | Repressor protein IclR | 0.08 ± 0.01 | 0.56 ± 0.005 |
| phoH | PhoH protein | 0.5 ± 0.07 | 0.08 ± 0.005 |
| psd | Phosphatidylserine decarboxylase precursor | 0.32 ± 0 | 0.43 ± 0.01 |
| rffH | Glucose-1-phosphate thymidylyltransferase | 0.2 ± 0.01 | 0.55 ± 0.05 |
| thil | Thiamin biosynthesis protein | 0.27 ± 0.09 | 1.7 ± 0.5 |
| thyA | Thymidylate synthase | 0.28 ± 0 | 0.45 ± 0.02 |
| truA | Pseudouridylate synthase I | 0.31 ± 0.01 | 0.7 ± 0.08 |
| Genes encoding proteins with diverse functions | |||
| dedA | DedA protein | 0.29 ± 0.02 | 0.45 ± 0.07 |
| dedE | DedE protein | 0.3 ± 0.025 | 0.5 ± 0.09 |
| dinG | Probable ATP-dependent helicase DinG | 0.24 ± 0.003 | 1.4 ± 0.13 |
| dnaG | DNA primase | 0.2 ± 0.015 | 1.1 ± 0.13 |
| fkpA | FkpA protein | 0.29 ± 0.005 | 0.47 ± 0.005 |
| fldB | Flavodoxin | 0.32 ± 0.005 | 1.26 ± 0 |
| ftsH | Cell division protein FtsH, protease | 0.25 ± 0.01 | 0.9 ± 0.06 |
| ftsJ/rrmJ | Cell division protein, 23S rRNA methyltransferase | 0.29 ± 0.015 | 1.2 ± 0.12 |
| ftsK | Cell division protein FtsK | 0.2 ± 0.01 | 0.9 ± 0.07 |
| gidA | GidA protein | 0.24 ± 0.01 | 0.8 ± 0.09 |
| hflC | HflC protein | 0.22 ± 0.02 | 0.54 ± 0 |
| hflK | HflK protein | 0.25 ± 0.01 | 0.7 ± 0.06 |
| holA | DNA-directed DNA polymerase III delta chain | 0.31 ± 0.005 | 0.7 ± 0.12 |
| hscA | Heat shock cognate protein 66 | 0.09 ± 0.01 | 0.7 ± 0.13 |
| ksgA | Dimethyladenosine transferase | 0.24 ± 0.04 | 0.75 ± 0.07 |
| lepA | GTP-binding protein LepA | 0.28 ± 0.02 | 0.5 ± 0.03 |
| mrcA | Penicillin-binding protein 1a (pbp-1a) | 0.28 ± 0.02 | 1.3 ± 0.01 |
| mrdB | Rod shape-determining protein MrdB | 0.18 ± 0.02 | 0.74 ± 0.02 |
| pepB | Peptidase B | 0.17 ± 0 | 0.3 ± 0.06 |
| priA | Primosomal replication factor Y | 0.27 ± 0.015 | 1.1 ± 0.3 |
| recB | Exodeoxyribonuclease V 135-kDa polypeptide | 0.22 ± 0.01 | 1.2 ± 0.03 |
| recC | Exodeoxyribonuclease V 125-kDa polypeptide | 0.32 ± 0.01 | 0.9 ± 0.06 |
| recJ | Single-stranded-DNA-specific exonuclease | 0.3 ± 0.02 | 1.2 ± 0.17 |
| rimM | 16S rRNA processing protein | 0.16 ± 0.005 | 0.47 ± 0 |
| mhA | Ribonuclease HI | 0.26 ± 0.02 | 0.85 ± 0.15 |
| rpoA | DNA-directed RNA polymerase alpha chain | 0.23 ± 0.03 | 0.6 ± 0.03 |
| rpoB | DNA-directed RNA polymerase beta chain | 0.18 ± 0.005 | 0.4 ± 0.02 |
| rrmA | rRNA (guanine-N1)-methyltransferase | 0.25 ± 0.045 | 0.15 ± 0.025 |
| rtn | Rtn protein | 0.28 ± 0.01 | 1.65 ± 0.13 |
| sdiA | SdiA regulatory protein | 0.26 ± 0.025 | 0.44 ± 0.005 |
| sodA | Superoxide dismutase | 0.26 ± 0.01 | 0.07 ± 0.01 |
| tnpR | Resolvase | 0.08 ± 0.005 | 0.4 ± 0.1 |
| topA | DNA topoisomerase I | 0.23 ± 0.025 | 0.35 ± 0.04 |
| trmD | tRNA (guanine-n1)-methyltransferase | 0.17 ± 0.005 | 0.42 ± 0.02 |