TABLE 4.
Genes downregulated upon exposure to ClO2 among over- and underrepresented JCVI role categoriesa
| Locus tagb | Gene name | Annotationc | Fold change | Adjusted P value |
|---|---|---|---|---|
| Cell envelope | ||||
| lmo0198 | gcaD | Highly similar to UDP-N-acetylglucosamine pyrophosphorylase | 1.604 | 0 |
| lmo0695 | Unknown | 1.88 | 0.01 | |
| lmo0971 | dltD | DltD protein for d-alanine esterification of lipoteichoic acid and wall teichoic acid | 1.959 | 0.05 |
| lmo0972 | dltC | d-Alanyl carrier protein | 2.081 | 0 |
| lmo0973 | dltB | DltB protein for d-alanine esterification of lipoteichoic acid and wall teichoic acid | 2.265 | 0 |
| lmo1082 | Similar to dTDP-sugar epimerase | 1.749 | 0.01 | |
| lmo1548 | mreB | Similar to cell-shape determining protein MreB | 1.977 | 0 |
| lmo2038 | murE | Similar to UDP-N-acetylmuramoylalanyl-d-glutamate-2,6-diaminopimelate ligase | 1.793 | 0.04 |
| lmo2549 | gtcA | Wall teichoic acid glycosylation protein GtcA | 1.774 | 0.02 |
| Cellular processes | ||||
| lmo0217 | Similar to B. subtilis DivIC protein | 1.955 | 0.01 | |
| lmo0677 | Similar to flagellar biosynthesis protein FliQ | 4.934 | 0 | |
| lmo0679 | Similar to flagellar biosynthetic protein FlhB | 1.934 | 0.02 | |
| lmo0693 | Similar to flagellar motor switch protein FliY C-terminal part | 1.506 | 0.04 | |
| lmo0696 | Similar to flagellar hook assembly protein | 1.731 | 0.02 | |
| lmo1071 | Similar to cell division protein RodA and FtsW | 1.885 | 0.01 | |
| lmo1297 | Similar to aluminum resistance protein and to B. subtilis YnbB protein (hypothetical) | 1.604 | 0.05 | |
| lmo1364 | cspL | Similar to cold shock protein | 1.808 | 0 |
| lmo1544 | minD | Highly similar to cell division inhibitor (septum placement) protein MinD | 1.594 | 0.02 |
| lmo1699 | Some similarities to methyl-accepting chemotaxis proteins | 2.075 | 0 | |
| lmo1700 | Unknown | 1.782 | 0.03 | |
| lmo2040 | ftsL | Similar to cell division protein FtsL | 1.738 | 0.02 |
| lmo2427 | Similar to cell division proteins RodA, FtsW | 1.73 | 0.05 | |
| lmo2428 | Similar to cell division proteins RodA, FtsW | 1.996 | 0.01 | |
| lmo2506 | ftsX | Highly similar to cell division protein FtsX | 1.81 | 0.03 |
| lmo2507 | ftsE | Highly similar to the cell division ATP-binding protein FtsE | 1.828 | 0.01 |
| lmo2569 | Similar to dipeptide ABC transporter (dipeptide-binding protein) | 1.635 | 0.04 | |
| Energy metabolism | ||||
| lmo1072 | pycA | Highly similar to pyruvate carboxylase | 1.521 | 0.04 |
| lmo2367 | pgi | Glucose-6-phosphate isomerase | 1.597 | 0.01 |
| Fatty acid and phospholipid metabolism | ||||
| lmo0970 | Similar to enoyl-acyl-carrier protein reductase | 1.634 | 0.02 | |
| lmo1806 | acpA | Highly similar to acyl carrier proteins | 2.068 | 0.01 |
| lmo1807 | fabG | Similar to 3-ketoacyl-acyl-carrier protein reductase | 1.828 | 0.01 |
| lmo2202 | Similar to 3-oxoacyl-acyl-carrier protein synthase | 2.412 | 0 | |
| lmo2450 | Similar to carboxylesterase | 1.803 | 0.02 | |
| Protein synthesis | ||||
| lmo0177 | metS | Methionyl-tRNA synthetase | 1.811 | 0 |
| lmo0244 | Similar to ribosomal protein L33 type II | 1.944 | 0 | |
| lmo0695 | Unknown | 1.88 | 0.01 | |
| lmo1294 | miaA | Similar to tRNA isopentenylpyrophosphate transferase | 2.196 | 0.01 |
| lmo1658 | rpsB | 30S ribosomal protein S2 | 1.55 | 0.03 |
| lmo1755 | gatA | Glutamyl-tRNA (Gln) amidotransferase (subunit A) | 1.506 | 0.02 |
| lmo2047 | rpmF | Ribosomal protein L32 | 2.195 | 0 |
| lmo2597 | rplM | Ribosomal protein L13 | 2.077 | 0 |
| lmo2633 | rpsJ | Ribosomal protein S10 | 1.523 | 0.02 |
| lmo2811 | Similar to GTPase | 1.727 | 0.02 | |
| lmo2856 | rpmH | Ribosomal protein L34 | 1.979 | 0.02 |
| Purines, pyrimidines, nucleosides, and nucleotides | ||||
| lmo1827 | Similar to guanylate kinases | 1.771 | 0 | |
| lmo1929 | ndk | Similar to nucleoside diphosphate kinase | 2.104 | 0 |
| lmo0509 | prs | Similar to phosphoribosyl pyrophosphate synthetase | 1.768 | 0.01 |
| lmo1096 | guaA | Highly similar to GMP synthetase | 2.904 | 0 |
| lmo1929 | ndk | Similar to nucleoside diphosphate kinase | 2.104 | 0 |
| lmo1463 | Similar to cytidine deaminase | 1.75 | 0.01 | |
| lmo1885 | Similar to xanthine phosphoribosyltransferase | 2.201 | 0.01 | |
| Unknown function | ||||
| lmo1240 | Conserved hypothetical protein, similar to B. subtilis YsnB protein | 1.763 | 0 | |
| lmo0998 | Similar to hypothetical protein | 1.914 | 0.02 | |
| lmo1067 | Similar to GTP-binding elongation factor | 2.936 | 0 | |
| lmo1479 | lepA | Highly similar to GTP-binding protein LepA | 1.544 | 0.01 |
| lmo1500 | Similar to unknown proteins | 2.351 | 0.02 | |
| lmo2779 | Similar to probable GTP-binding protein | 2.916 | 0 | |
| lmo2802 | gidB | GidB protein | 1.511 | 0.03 |
a
All genes that showed a lower transcript level in the ClO2-exposed samples over the control sample without treatment are listed with an adjusted P value < 0.05 and a fold-change of ≥1.50. Only genes categorized into JCVI role categories with over- and underrepresentation on the basis of the odds ratio are listed.
b
Locus tag identification is on the basis of the lmo number from the L. monocytogenes EGD-e strain.
c
Annotation was defined on the basis of the JCVI role category listings.