TABLE 2.
Relative expression levels of Escherichia coli genes grown in a 1% WTE-containing medium as determined by Affymetrix microarray and qRT-PCR analyses
| Locus tag | Genea | Fold change
|
Gene function (cellular role[s])b | |
|---|---|---|---|---|
| Microarray | qRT-PCR | |||
| b1743 | spyc | 17.5 | 493.5 | Periplasmic protein related to spheroblast formation (unclassified) |
| b2074 | mdtAc | 4.5 | 35.9 | Multidrug efflux system, subunit A (cellular processes; toxin production and resistance) |
| b2075 | mdtB | 4.4 | 24.8 | Multidrug efflux system, subunit B (cellular processes; toxin production and resistance) |
| b2076 | mdtC | 2.1 | 15.3 | Multidrug efflux system, subunit C (cellular processes; toxin production and resistance) |
| b2077 | mdtD | 3.8 | 27.6 | Multidrug efflux system, subunit D (cellular processes; toxin production and resistance) |
| b1531 | marA | 6.3 | 22.5 | Multiple antibiotic resistance; transcriptional activator of defense systems (cellular processes; toxin production and resistance) |
| b1532 | marB | 2.6 | 21.5 | Multiple antibiotic resistance protein (cellular processes; toxin production and resistance) |
| b1530 | marR | 2.6 | 27.4 | DNA-binding transcriptional repressor of multiple antibiotic resistance (cellular processes; toxin production and resistance) |
| b0005 | yaaX | 4.9 | 26.6 | Hypothetical protein (unclassified) |
| b2390 | ypeC | 2.8 | 20.5 | Hypothetical protein (unclassified) |
| b0618 | citC | 34.6 | 14.7 | Citrate lyase synthetase (energy metabolism; TCA cycle) |
| b3687 | ibpA | 6.9 | 10.4 | Heat shock chaperone (protein fate; protein folding and stabilization) |
| b3686 | ibpB | 9.5 | 48.0 | Heat shock chaperone (protein fate; protein folding and stabilization) |
| b3238 | yhcN | 3.1 | 7.9 | Hypothetical protein (unclassified) |
| b2675 | nrdE | 26.8 | 5.2 | Ribonucleoside-diphosphate reductase (purines, pyrimidines, nucleosides, and nucleotides; 2′-deoxyribonucleotide metabolism) |
| b3119 | tdcR | 13.1 | 4.7 | Threonine dehydratase operon activator protein (unclassified) |
| b1306 | pspC | 3.6 | 4.6 | Phage shock protein: activates phage shock-protein expression (unclassified) |
| b3265 | acrE | 12.1 | 3.1 | Membrane fusion protein (cell envelope; biosynthesis and degradation of murein sacculus and peptidoglycan) |
| b3071 | yqjI | 2.9 | 2.1 | Predicted transcriptional regulator (unclassified) |
| b0929 | ompF | 0.1 | 0.04 | Outer membrane protein 1a (transport and binding proteins; porins) |
| b3056d | cca | 1.0 | 1.0 | tRNA nucleotidyl transferase (protein synthesis tRNA and rRNA base modification) |
| b4361d | dnaC | 1.1 | 0.9 | DNA biosynthesis protein (viral functions; general) |
| b2871e | ygeX | 27.1 | 0.9 | Putative diaminopropionate ammonia-lyase (energy metabolism; amino acids and amines) |
| b2971e | yghG | 17.5 | 0.4 | Hypothetical protein (unclassified) |
| b3948e | yijI | 28.6 | 1.4 | Hypothetical protein (NCBI record discontinued) |
| b0303e | ykgI | 13.2 | 0.4 | Hypothetical protein (unclassified) |
| b0519e | ylbE | 26.2 | 1.1 | Pseudogene (unclassified) |
a
Based on information from the NCBI genome resources (http://www.ncbi.nlm.nih.gov/genomes/lproks.cgi).
b
Based on information from TIGR Cellular Role Category (http://cmr.tigr.org/tigr-scripts/CMR/CmrHomePage.cgi).
c
BaeR consensus binding region upstream of the gene.
d
Constitutively expressed control genes.
e
Genes for which there was no correlation between the microarray and qRT-PCR data.