Table 2. Core set of genes upregulated (>2-fold) across multiple (≥4) growth phases in L. monocytogenes cells at 4°C vs. 20°C.
| EGD ORF | EGD description | Gene abbr. | Strand | EGD-e ORF | Cluster memb-ership | Log2 DE across five growth phases | ||||
|---|---|---|---|---|---|---|---|---|---|---|
| G1 | G2 | G3 | G4 | G5 | ||||||
| LMON_0187 | Veg protein | + | lmo0189 | 16/14 | 2.96 | 2.45 | 2.28 | 2.38 | 1.54 | |
| LMON_0209 | LSU ribosomal protein L25p | ctc | + | lmo0211 | 10 | 2.16 | 3.43 | 2.72 | 0.87 | 1.58 |
| LMON_0260 | Internalin H | inlH | + | lmo0263 | 12 | 2.21 | 3.67 | 2.11 | -1.54 | 1.57 |
| LMON_0261 | Internalin D | inlD | + | 9 | 1.86 | 2.79 | 2.18 | 1.23 | 2.70 | |
| LMON_0350 | Transaldolase | lmo0343 | 5 | 1.88 | 2.03 | 1.56 | 0.27 | 4.16 | ||
| LMON_0351 | 3-oxoacyl-[acyl-carrier protein] reductase | lmo0344 | 5 | 2.35 | 1.71 | 1.30 | 0.62 | 4.34 | ||
| LMON_0352 | Ribose 5-phosphate isomerase B | lmo0345 | 5 | 2.75 | 2.30 | 1.25 | 0.26 | 4.61 | ||
| LMON_0353 | Triosephosphate isomerase | lmo0346 | 5 | 2.38 | 1.95 | 1.75 | 0.45 | 4.38 | ||
| LMON_0354 | Phosphoenolpyruvate-dihydroxyacetone phosphotransferase, ADP-binding subunit DhaL | lmo0347 | 5 | 2.21 | 2.08 | 1.70 | 0.03 | 4.21 | ||
| LMON_0355 | Phosphoenolpyruvate-dihydroxyacetone phosphotransferase, dihydroxyacetone binding subunit DhaK | lmo0348 | 5 | 2.34 | 1.85 | 1.60 | 0.26 | 4.50 | ||
| LMON_0356 | Hypothetical protein | lmo0349 | 5 | 1.94 | 2.17 | 1.35 | -0.16 | 5.37 | ||
| LMON_0357 | Hypothetical protein | lmo0350 | 5 | 3.01 | 1.62 | 1.45 | -0.25 | 5.55 | ||
| LMON_0358 | Phosphoenolpyruvate-dihydroxyacetone phosphotransferase, subunit DhaM | lmo0351 | 5 | 2.49 | 1.79 | 1.57 | -0.37 | 5.50 | ||
| LMON_0360 | Acetyltransferase, GNAT family | + | lmo0353 | 12 | 1.85 | 1.50 | 1.23 | 0.67 | 1.72 | |
| LMON_0441 | Internalin A | inlA | + | lmo0433 | 5 | 2.01 | 1.82 | 1.92 | 1.62 | 2.30 |
| LMON_0486 | LSU ribosomal protein L32p | rpmF | + | lmo0486 | 19 | 1.43 | 1.46 | 1.76 | 1.75 | 1.22 |
| LMON_0515 | Universal stress protein | + | lmo0515 | 12 | 1.34 | 1.76 | 1.12 | -2.06 | 1.98 | |
| LMON_0561 | Phosphoribosyl-ATP pyrophosphatase | hisE | lmo0561 | 2 | 1.70 | 1.64 | 1.01 | 1.53 | 2.98 | |
| LMON_0611 | Internalin-like protein | lmo0610 | 12 | 2.50 | 2.85 | 2.06 | -0.73 | 2.19 | ||
| LMON_0625 | Acetyltransferase, GNAT family | lmo0624 | 5 | 2.07 | 2.19 | 1.67 | 1.33 | 4.46 | ||
| LMON_0626 | Hypothetical protein | lmo0625 | 5 | 2.18 | 2.19 | 1.59 | 1.23 | 4.43 | ||
| LMON_0785 | PTS system, mannose-specific IID component | lmo0781 | 12 | 1.81 | 2.76 | 1.32 | -0.54 | 1.97 | ||
| LMON_0786 | PTS system, mannose/fructose-specific IIC component | lmo0782 | 12 | 1.60 | 2.72 | 1.43 | -0.76 | 1.64 | ||
| LMON_0787 | PTS system, mannose-specific IIB component | lmo0783 | 12 | 1.86 | 2.80 | 1.43 | -1.11 | 1.86 | ||
| LMON_0788 | PTS system, mannose-specific IIB component / IIA component | lmo0784 | 12 | 2.05 | 3.10 | 1.49 | -1.23 | 1.70 | ||
| LMON_0920 | Succinate-semialdehyde dehydrogenase [NAD] | + | lmo0913 | 10 | 4.64 | 5.74 | 2.96 | 0.40 | 2.35 | |
| LMON_0944 | Hypothetical protein | 10 | 2.77 | 3.84 | 4.22 | 1.39 | 2.00 | |||
| 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_1932 | Predicted membrane protein hemolysin III | + | lmo1864 | 14 | 2.21 | 1.58 | 1.78 | 1.84 | 1.06 | |
| LMON_2054 | Dihydroxy-acid dehydratase | ilvD | + | lmo1983 | 4* | 3.52 | 3.89 | 3.34 | 4.29 | 3.62 |
| LMON_2055 | Acetolactate synthase large subunit | ilvB | + | lmo1984 | 3/15 | 3.67 | 4.17 | 3.41 | 4.41 | 4.37 |
| LMON_2056 | Acetolactate synthase small subunit | ilvH | + | lmo1985 | 15/1 | 3.67 | 4.02 | 3.39 | 4.41 | 4.03 |
| LMON_2057 | Ketol-acid reductoisomerase | ilvC | + | lmo1986 | 4 | 2.98 | 4.08 | 3.00 | 3.96 | 3.28 |
| LMON_2058 | 2-isopropylmalate synthase | leuA | + | lmo1987 | 11 | 3.41 | 3.68 | 2.74 | 3.56 | 3.87 |
| LMON_2059 | 3-isopropylmalate dehydrogenase | leuB | + | lmo1988 | 3 | 3.18 | 3.60 | 2.86 | 3.84 | 4.72 |
| LMON_2060 | 3-isopropylmalate dehydratase large subunit | leuC | + | lmo1989 | 3 | 3.29 | 3.48 | 2.72 | 3.72 | 5.25 |
| LMON_2061 | 3-isopropylmalate dehydratase small subunit | leuD | + | lmo1990 | 3 | 3.16 | 3.64 | 2.71 | 3.96 | 5.70 |
| LMON_2062 | Threonine dehydratase | ilvA | + | lmo1991 | 3 | 3.16 | 3.65 | 2.50 | 3.86 | 5.58 |
| LMON_2234 | Hypothetical protein | lmo2158 | 12 | 3.80 | 5.25 | 3.18 | 0.77 | 3.03 | ||
| LMON_2407 | Internalin-like protein | + | lmo2396 | 3 | 1.13 | 1.52 | 0.92 | 1.30 | 2.67 | |
| LMON_2696 | Universal stress protein | + | lmo2673 | 12 | 3.09 | 3.64 | 1.90 | -0.77 | 4.24 | |
| LMON_2718 | Phosphoenolpyruvate-dihydroxyacetone phosphotransferase, dihydroxyacetone binding subunit DhaK | + | lmo2695 | 12 | 2.73 | 3.82 | 2.25 | -0.43 | 2.36 | |
| LMON_2719 | Phosphoenolpyruvate-dihydroxyacetone phosphotransferase, ADP-binding subunit DhaL | + | lmo2696 | 12 | 2.76 | 3.76 | 2.13 | 0.31 | 2.61 | |
| LMON_2720 | Phosphoenolpyruvate-dihydroxyacetone phosphotransferase, subunit DhaM; | + | lmo2697 | 12 | 2.46 | 3.79 | 2.13 | 0.58 | 2.82 | |
| LMON_2735 | Secreted protein | lmo2713 | 1 | 2.10 | 1.16 | 1.12 | 1.69 | 2.03 | ||
| LMON_2770 | general stress protein 26 | lmo2748 | 12 | 2.51 | 3.72 | 1.71 | -1.81 | 1.98 | ||
| LMON_2800 | PTS system, cellobiose-specific IIA component | lmo2780 | 12 | 1.79 | 1.57 | 1.45 | -0.55 | 2.57 | ||
| LMON_2801 | Beta-glucosidase | lmo2781 | 12 | 2.06 | 1.38 | 1.45 | -1.18 | 2.27 | ||
| LMON_2802 | PTS system, cellobiose-specific IIB component | lmo2782 | 12 | 2.11 | 1.49 | 1.81 | -1.48 | 2.44 | ||
| LMON_2803 | PTS system, cellobiose-specific IIC component | lmo2783 | 12 | 2.32 | 1.24 | 1.80 | -1.99 | 2.05 | ||
* 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.