TABLE 1.
PQ-regulated genesa
| Gene type | No. | Gene | Ratio | Description |
|---|---|---|---|---|
| PQ-activated | b0463 | acrA | 2.0 | AcrAB efflux system effects Mar multiple resistance |
| b0605 | ahpC | 2.8 | Alkyl hydroperoxide reductase small subunit | |
| b1415 | aldA | 2.3 | Aldehyde dehydrogenase, NAD linked | |
| b0863 | artI | 1.9 | Periplasmic binding protein of Arg transport system | |
| b0864 | artP | 1.9 | Arg periplasmic transport system | |
| b0710 | b0710 | 2.0 | Function unknown | |
| b1378 | b1378 | 1.7 | Putative pyruvate-flavodoxin oxidoreductase | |
| b1452 | b1452 | 1.9 | Function unknown | |
| b2351 | b2351 | 1.7 | CPS-53 prophage; putative bactoprenol glucosyl transferase | |
| b2962 | b2962 | 2.4 | Function unknown | |
| b4131 | cadA | 1.8 | Lysine decarboxylase | |
| b4133 | cadC | 2.4 | Regulatory gene | |
| b2198 | ccmD | 1.7 | Cytochrome c-related | |
| b0429 | cyoD | 1.7 | Cytochrome o oxidase subunit IV | |
| b2752 | cysD | 1.7 | Sulfate adenylyltransferase | |
| b2414 | cysK | 1.9 | Cysteine synthase A | |
| b1190 | dadX | 1.7 | Alanine racemase | |
| b4383 | deoB | 1.9 | Deoxyribouratase, phosphopentomutase | |
| b0184 | dnaE | 2.0 | DNA polymerase III, alpha subunit | |
| b0812 | dps | 1.7 | Stress response DNA-binding protein | |
| b0684 | fldA | 4.7 | Flavodoxin | |
| b3288 | fmt | 1.8 | Methionyl-tRNA formyltransferase | |
| b3924 | fpr | 3.6 | Ferredoxin NADP+ reductase; anaerobic | |
| b1611 | fumC | 6.9 | Fumarase C | |
| b0683 | fur | 2.2 | Ferric iron uptake, negative regulatory gene | |
| b2094 | gatA | 2.9 | Galactitol-specific enzyme IIA of PTSb | |
| b2093 | gatB | 3.7 | Galactitol-specific enzyme IIB of PTS | |
| b2091 | gatD | 1.7 | Galactitol-1-phosphate dehydrogenase | |
| b0450 | glnK | 1.8 | Regulated through NRI/NRII two-component regulatory system | |
| b0720 | gltA | 3.1 | Citrate synthase | |
| b2552 | hmpA | 1.8 | Dihydropteridine reductase 2 and nitric oxide dioxygenase NAD/FAD activity | |
| b0440 | hupB | 1.7 | Histone-like protein HU-alpha, HU-1 | |
| b2237 | inaA | 2.9 | Function unknown | |
| b4036 | lamB | 4.8 | Maltose high-affinity uptake | |
| b0096 | lpxC | 2.0 | Cell envelope and cell separation | |
| b4034 | malE | 2.1 | Maltose-binding protein, periplasmic; transport and chemotaxis | |
| b4035 | malK | 1.9 | Maltose transport complex, ATP-binding subunit | |
| b0168 | map | 1.7 | Methionine aminopeptidase | |
| b1531 | marA | 2.6 | Transcription activator of multiple-antibiotic-resistance system | |
| b0086 | murF | 1.7 | d-Alanyl:d-alanine-adding enzyme | |
| b0578 | nfnB | 2.1 | Resistance to nitrofurantoin; a nitroreductase | |
| b2281 | nuoI | 1.8 | NADH dehydrogenase I subunit | |
| b2279 | nuoK | 1.9 | NADH dehydrogenase I subunit | |
| b0113 | pdhR | 1.9 | Pyruvate-dehydrogenase repressor | |
| b4025 | pgi | 2.1 | Glucose phosphate isomerase | |
| b1101 | ptsG | 3.3 | PTS family enzyme IIC, glucose-specific | |
| b1658 | purR | 1.9 | Purine repressor | |
| b3317 | rplB | 1.9 | 50S ribosomal subunit protein L2 | |
| b3319 | rplD | 2.5 | 50S ribosomal subunit protein L4 | |
| b3305 | rplF | 1.7 | 50S ribosomal subunit protein L6 | |
| b3985 | rplJ | 1.7 | 50S ribosomal subunit protein L10 | |
| b3318 | rplW | 1.8 | 50S ribosomal subunit protein L23 | |
| b3312 | rpmC | 1.7 | 50S ribosomal subunit protein L29 | |
| b3314 | rpsC | 1.7 | 30S ribosomal subunit protein S3 | |
| b3321 | rpsJ | 2.0 | 30S ribosomal subunit protein S10 | |
| b3316 | rpsS | 1.7 | 30S ribosomal subunit protein S19 | |
| b0724 | sdhB | 1.8 | Succinate dehydrogenase iron-sulfur protein | |
| b3908 | sodA | 12.3 | Superoxide dismutase, Mn | |
| b4062 | soxS | 2.3 | Regulatory protein of soxRS regulon | |
| b0729 | sucD | 1.9 | Succinyl-coenzyme A synthetase alpha subunit | |
| b3708 | tnaA | 2.4 | Tryptophanase | |
| b0850 | ybjC | 1.7 | Function unknown | |
| b2523 | yfhI | 1.9 | Peptidase B; aminopeptidase | |
| b3520 | yhjB | 3.4 | Putative transcriptional regulator (LuxR/UhpA family) | |
| b4217 | ytfK | 2.3 | Function unknown | |
| b1852 | zwf | 2.7 | Glucose-6-phosphate dehydrogenase | |
| PQ-down-regulated | b3237 | argR | 0.6 | Repressor of Arg regulon |
| b4139 | aspA | 0.5 | Aspartate ammonia-lyase (aspartase) | |
| b0218 | b0218 | 0.3 | Function unknown | |
| b0271 | b0271 | 0.5 | Function unknown | |
| b0938 | b0938 | 0.6 | Function unknown | |
| b1029 | b1029 | 0.4 | Function unknown | |
| b1567 | b1567 | 0.6 | Qin prophage | |
| b1903 | b1903 | 0.5 | Function unknown | |
| b2102 | b2102 | 0.5 | Function unknown | |
| b2355 | b2355 | 0.5 | Function unknown | |
| b2629 | b2629 | 0.4 | Function unknown | |
| b2768 | b2768 | 0.6 | Function unknown | |
| b0032 | carA | 0.5 | Carbamoylphosphate synthase (glutamine-hydrolyzing) light subunit | |
| b0620 | criR | 0.5 | Response regulator in two-component regulatory system with DpiB | |
| b1575 | dicB | 0.5 | Control of cell division. Activates MinC | |
| b2369 | evgA | 0.6 | Multicopy on plasmid in strain with a deletion of envZ induces ompC expression | |
| b2323 | fabB | 0.4 | Beta-ketoacyl-acyl carrier protein synthase I | |
| b1925 | fliS | 0.5 | Flagellar synthesis; flagellar regulon member | |
| b2025 | hisF | 0.5 | Cyclase component of IGP synthase complex | |
| b3580 | lyxK | 0.5 | l-Xylulose kinase, cryptic | |
| b0923 | mukE | 0.5 | Involved in chromosome partitioning | |
| b1224 | narG | 0.3 | Nitrate reductase alpha subunit | |
| b3480 | nikE | 0.6 | Formate hydrogen-lyase activity | |
| b0929 | ompF | 0.2 | Outer membrane protein, porin | |
| b4245 | pyrB | 0.3 | Aspartate transcarbamylase, catalytic subunit | |
| b0945 | pyrD | 0.5 | Dihydroorotate oxidase | |
| b4387 | smp | 0.6 | Membrane protein | |
| b1656 | sodB | 0.5 | Superoxide dismutase, Fe | |
| b1646 | sodC | 0.6 | Superoxide dismutase, Cu, Zn | |
| b2497 | uraA | 0.4 | Uracil concentration dependence of pyr mutants; Ura ABC transporter | |
| b0193 | yaeF | 0.4 | Function unknown | |
| b0315 | yahA | 0.6 | Putative transcriptional repressor (LuxR/UhpA family) | |
| b1347 | ydaC | 0.6 | Rac prophage | |
| b2597 | yfiA | 0.5 | Ribosome-associated factor, stabilizes ribosomes against dissociation | |
| b3087 | ygjR | 0.4 | Putative NADP-binding dehydrogenase | |
| b3088 | ygjT | 0.5 | Putative transmembrane protein | |
| b3112 | yhaQ | 0.4 | Anaerobic pathway, l-serine deaminase, l-serine dehydratase | |
| b3516 | yhiX | 0.5 | Putative transcriptional regulator (AraC/XylS family) | |
| b3582 | yiaR | 0.5 | Putative hexulose-6-phosphate isomerase | |
| b3879 | yihR | 0.6 | Putative aldose-1-epimerase | |
| b3888 | yiiD | 0.5 | Putative acyltransferase | |
| b4048 | yjbM | 0.5 | Function unknown | |
| b4333 | yjiK | 0.6 | Putative outer membrane protein | |
| b4337 | yjiO | 0.4 | Putative transport protein | |
| b4380 | yjjI | 0.6 | Function unknown | |
| b4394 | yjjX | 0.4 | Function unknown |
a
No., unique identifier. Boldface denotes genes modulated by either exposure to PQ or expression of SoxS. Underlining denotes previously characterized soxRS genes.
b
PTS, phosphotransferase system.