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. 2017 Jun 29;12(6):e0180123. doi: 10.1371/journal.pone.0180123

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.