Table 6. Genes commonly associated with the L. monocytogenes CSR.
| EGD ORF | EGD description | Gene abbr. | Strand | EGD-e ORF | Cluster memb-ership | Log2 DE across five growth phases | ||||
|---|---|---|---|---|---|---|---|---|---|---|
| G1 | G2 | G3 | G4 | G5 | ||||||
| Osmolyte and oligopeptide uptake | ||||||||||
| LMON_1024 | Glycine betaine ABC transport system, ATP-binding protein | gbuA | + | lmo1014 | 8 | 0.15 | 0.56 | 0.82 | 1.68 | -0.69 |
| LMON_1025 | Glycine betaine ABC transport system, permease protein | gbuB | + | lmo1015 | 19 | 0.04 | 0.48 | 0.75 | 1.14 | 0.08 |
| LMON_1026 | Glycine betaine ABC transport system, glycine betaine-binding protein | gbuC | + | lmo1016 | 15 | 0.10 | 0.54 | 0.64 | 0.87 | 0.71 |
| LMON_1488 | Osmotically activated L-carnitine/choline ABC transporter, permease protein OpuCD | opuCD | − | lmo1425 | 10 | 2.34 | 5.37 | 3.52 | 1.79 | 1.29 |
| LMON_1489 | Osmotically activated L-carnitine/choline ABC transporter, substrate-binding protein OpuCC | opuCC | − | lmo1426 | 10 | 2.45 | 5.23 | 3.78 | 1.82 | 1.24 |
| LMON_1490 | Osmotically activated L-carnitine/choline ABC transporter, permease protein OpuCB | opuCB | − | lmo1427 | 10 | 2.51 | 5.28 | 3.78 | 1.58 | 1.10 |
| LMON_1491 | Osmotically activated L-carnitine/choline ABC transporter, ATP-binding protein OpuCA | opuCA | − | lmo1428 | 10 | 2.63 | 5.54 | 3.94 | 1.30 | -0.01 |
| LMON_2268 | Oligopeptide transport ATP-binding protein OppF | oppF | − | lmo2192 | 2 | -0.56 | -0.61 | -0.43 | -0.39 | 1.39 |
| LMON_2269 | Oligopeptide transport ATP-binding protein OppD | oppD | − | lmo2193 | 2 | -0.59 | -0.74 | -0.38 | -0.30 | 0.91 |
| LMON_2270 | Oligopeptide transport system permease protein OppC | oppC | − | lmo2194 | 15* | -0.66 | -0.91 | -0.35 | -0.15 | -0.29 |
| LMON_2271 | Oligopeptide transport system permease protein OppB | oppB | − | lmo2195 | 19 | -0.61 | -0.85 | -0.35 | 0.09 | -0.79 |
| LMON_2272 | Oligopeptide ABC transporter, periplasmic oligopeptide-binding protein OppA | oppA | − | lmo2196 | 9 | -0.67 | 0.00 | -0.46 | -1.44 | -0.17 |
| RNA and DNA repair | ||||||||||
| LMON_0004 | Hypothetical protein | + | lmo0004 | 16 | 1.25 | 0.69 | 0.54 | -0.29 | -0.69 | |
| LMON_0005 | DNA recombination and repair protein RecF | recF | + | lmo0005 | 16 | 1.40 | 0.74 | 0.59 | 0.06 | -0.15 |
| LMON_0006 | DNA gyrase subunit B | gyrB | + | lmo0006 | 20 | 1.24 | 0.53 | 0.49 | -0.15 | 0.45 |
| LMON_0007 | DNA gyrase subunit A | gyrA | + | lmo0007 | 20 | 1.17 | 0.61 | 0.40 | -0.10 | 1.15 |
| LMON_0846 | Endoribonuclease L-PSP | + | lmo0844 | 7/6/10 | 0.53 | 1.18 | 1.11 | 0.24 | -0.41 | |
| LMON_0848 | Excinuclease ABC subunit C | + | lmo0846 | 15 | -0.44 | -0.04 | 0.15 | 1.76 | 1.12 | |
| LMON_0869 | Cold-shock DEAD-box protein A | + | lmo0866 | 14 | 1.97 | 0.85 | 0.38 | 1.87 | 0.45 | |
| LMON_1037 | Ribonuclease J1 (endonuclease and 5' exonuclease) | − | lmo1027 | 16 | 1.71 | 0.33 | -0.03 | -0.10 | -1.17 | |
| LMON_1225 | DNA polymerase X family | + | lmo1231 | 2 | 1.12 | 0.22 | 0.42 | 0.76 | 2.10 | |
| LMON_1305 | ATP-dependent RNA helicase YxiN | + | lmo1246 | 6 | 0.99 | 0.75 | 0.56 | 0.07 | -1.04 | |
| LMON_1317 | Hypothetical protein | + | lmo1256 | 12 | 2.04 | 1.68 | 1.00 | -1.20 | 2.14 | |
| LMON_1336 | DNA topoisomerase I | topA | + | lmo1275 | 4 | 0.02 | 0.74 | 0.30 | 1.00 | 0.31 |
| LMON_1348 | Topoisomerase IV subunit A | parC | + | lmo1287 | 2 | -0.02 | -0.06 | 0.19 | 0.10 | 1.39 |
| LMON_1461 | RecA protein | recA | + | lmo1398 | 12 | 0.73 | 1.27 | 0.34 | -0.27 | 0.46 |
| LMON_1513 | ATP-dependent RNA helicase YqfR | − | lmo1450 | 6 | 1.33 | 1.12 | 1.18 | 1.01 | -1.04 | |
| LMON_1787 | ATP-dependent RNA helicase YfmL | − | lmo1722 | 6 | 1.69 | 1.45 | 1.28 | 1.21 | 0.47 | |
| LMON_2342 | ATP-dependent nuclease, subunit A | − | lmo2267 | 17 | -0.99 | -0.77 | -0.35 | -0.62 | 1.77 | |
| LMON_2343 | ATP-dependent nuclease, subunit B | addB | − | lmo2268 | 17 | -0.78 | -0.45 | -0.11 | -0.60 | 1.42 |
| LMON_2778 | DNA topoisomerase III | topB | − | lmo2756 | 17 | -0.25 | -0.03 | 0.19 | -0.20 | 1.40 |
| LMON_2812 | DNA-binding protein | lmo2792 | 5 | 0.62 | 1.34 | 0.75 | -0.80 | 2.49 | ||
| Regulatory elements | ||||||||||
| LMON_0198 | Virulence regulatory factor PrfA | prfA | − | lmo0200 | 17 | -2.04 | -0.44 | 1.01 | 0.10 | 5.32 |
| LMON_0229 | Transcriptional regulator CtsR | ctsR | + | lmo0229 | 16 | 1.90 | 0.42 | 0.47 | -0.55 | 0.16 |
| LMON_0244 | RNA polymerase sigma factor SigH | sigH | + | lmo0243 | 7 | -1.29 | -0.60 | -0.49 | -0.59 | -2.35 |
| LMON_0431 | RNA polymerase sigma factor SigC | sigC | − | lmo0423 | 13 | -2.03 | -1.48 | -0.59 | -0.62 | -0.97 |
| LMON_0679 | Motility gene repressor MogR | mogR | − | lmo0674 | 16 | 0.62 | 0.02 | 0.03 | -1.20 | -0.72 |
| LMON_0900 | RNA polymerase sigma factor SigB | sigB | + | lmo0895 | 10 | 0.00 | 0.58 | 0.19 | -0.78 | -0.62 |
| LMON_1166 | Ethanolamine sensory transduction histidine kinase | + | lmo1173 | 5/2 | 1.03 | 0.71 | -0.03 | 0.06 | 2.43 | |
| LMON_1341 | GTP-sensing transcriptional pleiotropic repressor codY | codY | + | lmo1280 | 3 | -0.42 | 0.61 | 0.02 | 0.09 | 1.27 |
| LMON_1517 | RNA polymerase sigma factor RpoD | rpoD | − | lmo1454 | 5 | 0.08 | -0.24 | -0.60 | -0.88 | 0.54 |
| LMON_1539 | Heat-inducible transcription repressor HrcA | hrcA | − | lmo1475 | 16 | 1.42 | -0.02 | 0.10 | -0.28 | -0.43 |
| LMON_1807 | Two-component sensor histidine kinase BceS | cesK | − | lmo1741 | 2 | -0.17 | -0.17 | 0.02 | 0.03 | 2.05 |
| LMON_1811 | Two-component response regulator YvcP (VirR in L. monocytogenes 10403S) | virR | − | lmo1745 | 17 | -0.48 | -0.61 | -0.12 | -0.30 | 0.02 |
| LMON_2432 | Sensor histidine kinase | virS | − | lmo2421 | 14 | 1.27 | -0.03 | 0.28 | 0.89 | 0.17 |
| LMON_2472 | RNA polymerase sigma factor SigL | sigL | − | lmo2461 | 5 | -0.20 | -0.05 | -0.10 | -0.42 | 0.85 |
| LMON_2527 | Transcriptional regulator DegU | degU | − | lmo2515 | 16 | 1.61 | 0.62 | 0.54 | 0.04 | -0.94 |
| LMON_2702 | Osmosensitive K+ channel histidine kinase KdpD | kdpD | − | lmo2679 | 2 | 0.99 | 0.46 | 0.60 | 0.44 | 4.22 |
| Ribosome functions | ||||||||||
| LMON_0209 | LSU ribosomal protein L25p | ctc | + | lmo0211 | 10 | 2.16 | 3.43 | 2.72 | 0.87 | 1.58 |
| LMON_0486 | LSU ribosomal protein L32p | rpmF | + | lmo0486 | 19 | 1.43 | 1.46 | 1.76 | 1.75 | 1.22 |
| LMON_1388 | Translation initiation factor 2 | infB | + | lmo1325 | 2 | 0.55 | 0.09 | -0.01 | 0.39 | 1.16 |
| LMON_1390 | Ribosome-binding factor A | rbfA | + | lmo1327 | 2 | 0.59 | 0.16 | -0.03 | 0.25 | 1.75 |
| LMON_2523 | Ribosomal subunit interface protein | − | lmo2511 | 5 | 1.08 | 1.32 | 0.65 | -0.90 | 3.14 | |
| Cold-stress proteins | ||||||||||
| LMON_1427 | Cold-shock protein | cspL | + | lmo1364 | 16 | 1.58 | 1.34 | 0.45 | 0.12 | 0.27 |
| LMON_1947 | Cold shock protein CspD | cspD | + | lmo1879 | 12 | 0.96 | 1.00 | -0.09 | -3.93 | -1.96 |
| LMON_2087 | Cold shock protein CspB | cspB | − | lmo2016 | 16 | -3.67 | -4.42 | -5.85 | -7.83 | -2.97 |
| Additional proteins | ||||||||||
| LMON_0213 | Low temperature requirement B protein | ltrB | + | lmo0215 | 2 | 0.03 | -0.26 | -0.25 | 0.00 | 1.78 |
| LMON_0398 | Low temperature requirement protein A | ltrA | − | lmo0389 | 12* | 0.43 | -0.23 | 0.61 | -0.63 | 0.08 |
| LMON_0691 | Flagellar motor rotation protein MotB | motB | + | lmo0686 | 17 | -0.81 | -0.37 | 0.07 | -0.26 | 1.44 |
| LMON_0693 | Glycosyl transferase | gmaR | + | lmo0688 | 17 | -0.84 | -0.42 | -0.06 | -0.44 | 1.29 |
| LMON_0694 | Chemotaxis protein CheV | cheV | + | lmo0689 | 17 | -0.77 | -0.04 | -0.19 | -0.65 | 2.37 |
| LMON_0695 | Flagellin protein FlaA | flaA | + | lmo0690 | 5 | 0.58 | -1.03 | -0.70 | -2.00 | 1.16 |
| LMON_0950 | Non-specific DNA-binding protein Dps / Iron-binding ferritin-like antioxidant protein / Ferroxidase | fri | + | lmo0943 | 10 | 0.39 | 1.50 | 0.03 | -0.51 | -0.22 |
| LMON_2409 | Low temperature requirement C protein | ltrC | + | lmo2398 | 12 | 1.14 | 1.21 | 0.75 | -1.61 | 0.16 |
* indicates <0.50 cluster membership; G1–G5 refer to differential expression in L. monocytogenes cells grown at 4°C relative to 20°C and across five specific growth phases (see Fig 1); Blue shading indicates genes with significantly increased (> 1log2, p<0.05) gene expression and yellow shading indicates genes with significantly decreased (< -1log2, p<0.05) expression at 4°C relative to 20°C; Bolded values indicate significant (p<0.05) differential expression changes.