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Table 5 Expression profile of genes belonging to PHA biosynthesis and central metabolic pathways in P. putida KT2440 under different conditions

From: Integrated analysis of gene expression and metabolic fluxes in PHA-producing Pseudomonas putida grown on glycerol

Gene name Locus tag Description Log2 change
CH vs. CL NH vs. NL NL vs. CL NH vs. CH
PHA synthesis
 phaI PP5008 PHA granule-associated −0.69 1.10 1.41 1.00
 phaF PP5007 PHA granule-associated −0.49 −0.89 1.11 0.72
 phaC1 PP5003 PHA polymerase −0.11 0 −0.25 −0.15
 phaC2 PP5005 PHA polymerase −0.27 −0.29 0.48 0.46
 phaZ PP5004 PHA depolymerase 0.30 −0.18 0.87 0.39
 phaD PP5006 Transcriptional regulator 0.19 −0.24 0.50 0.07
 phaG PP1408 Acyl-transferase 1.06 1.51 2.93 2.48
Glycerol metabolism
 oprB PP1019 Porin B transporter 0.76 0.37 −0.39 −0.78
 glpF PP1076 MIP family channel protein 0.15 0.78 1.28 −0.65
 glpK PP1075 Glycerol kinase 0.35 0.19 −0.72 −0.88
 glpR PP1074 Transcriptional regulator 0.81 0.40 −0.97 1.39
 glpD PP1073 Glycerol-3-P dehydrogenase −0.01 −0.48 0.05 −0.42
Embden–Meyerhof–Parnas pathway
 Glk PP1011 Glucokinase 0.76 0.25 −0.13 −0.65
 gltR PP1012 Transcriptional regulator 0.78 0.43 −0.7 1.05
PP1013 Integral membrane sensor 0.7 0.4 1.00 1.3
 Pgi PP1808 Glucose-6-phosphate isomerase 0.13 0.11 −0.10 0.13
 Fbp PP5040 Fructose-1,6-bisphosphatase 0.21 −0.12 −0.10 0.11
 Fda PP4960 Fructose-1,6-bisphosphate aldolase −0.13 0.24 −0.10 0.5
 tpiA PP4715 Triosephosphate isomerase 0.82 0.47 −0.10 −0.93
 gap1 PP1009 GAP dehydrogenase, type I 0.30 0.69 1.32 −0.92
 gap2 PP2149 GAP dehydrogenase, type II 0.14 −0.06 −0.10 0.42
 pgk PP4963 Phosphoglycerate kinase 0.08 0.37 −0.10 0.46
 pgm PP5056 Phosphoglyceromutase 0.25 0.24 −0.1 0.04
 eno PP1612 Phosphopyruvate hydratase 0.18 0.46 −0.1 0.07
 pyk PP1362 Pyruvate kinase 0.11 0.30 −0.1 0.85
Pentose phosphate pathways
 zwf1 PP1022 G6P dehydrogenase 1.33 0.39 0.85 −0.09
 zwf2 PP4042   0.48 0.14 −0.10 −0.48
 zwf3 PP5351   −0.23 −0.05 −0.10 0.21
 pgl PP1023 6-P-gluconate dehydrogenase 0.65 0.42 1.15 0.77
 gnd PP4043 6-P-gluconate dehydrogenase 0.08 −0.15 −0.1 −0.23
 gnuK PP3416 Carbohydrate kinase −0.06 −0.52 −0.10 −0.7
 kguK PP3378 Dehydroglucokinase −0.02 −0.63 −0.10 −0.21
 kguD PP3376 2-Ketogluconate 6-phosphate reductase −0.15 −0.17 −0.10 −0.2
 rpiA PP5150 Ribose-5-phosphate isomerase A −0.09 0.06 −0.10 0.06
 rpe PP0415 Ribulose-phosphate 3-epimerase −0.04 0.20 −0.74 −0.5
 tktA PP4965 Transketolase 0.28 0.29 −0.10 0.46
 tal PP2168 Transaldolase B −0.6 −0.07 −0.10 0.70
Entner-Doudoroff pathway
 edd PP1010 6-Phosphogluconate dehydratase 0.9 0.22 −0.03 −0.71
 eda PP1024 KDPG aldolase 1.24 0.29 1.65 0.98
Pyruvate metabolism
 acoA PP0555 Pyruvate dehydrogenase 1.16 1.86 1.03 −0.33
 acoB PP0554 Pyruvate dehydrogenase 1.5 1.88 1.04 −0.66
 acoC PP0553 Pyruvate dehydrogenase 1.57 1.81 −0.96 −0.72
PP0545 Aldehyde dehydrogenase 0.2 0.11 −0.91 −1.01
 acsA PP4487 Acetyl-CoA synthetase −0.13 0.23 −0.15 3.56
 accC-2 PP5347 Pyruvate carboxylase 0.22 −0.27 −0.12 0.07
 ppsA PP2082 Phosphoenolpyruvate synthase 0.10 0.22 −0.12 0.09
 ppc PP1505 Phosphoenolpyruvate carboxylase 0.09 −0.06 −0.10 0.50
PP0154 Acetyl-CoA hydrolase 0.21 0.23 1.42 1.41
TCA cycle
gltA PP4194 Citrate synthase 0.01 0.57 −0.10 1.12
acnA PP2112 Aconitate hydratase −0.04 −0.22 −0.10 −0.57
acnB PP2339 Aconitate hydratase −0.33 0.2 −0.10 0.74
icd PP4012 Isocitrate dehydrogenase 0.38 −0.14 −0.10 1.97
sucA PP4189 2-Oxoglutarate dehydrogenase 0.37 0.08 −0.10 −0.17
sucD PP4185 Succinyl-CoA synthetase sub alpha 0.6 0.35 −0.10 −0.13
sucC PP4186 Succinyl-CoA synthetase sub beta 0.47 0.35 −0.10 0.14
sdhA PP4191 Succinate dehydrogenase 0.24 0.30 −0.10 −0.04
fumC PP0944 Fumarate hydratase 2.46 −0.63 1.92 −0.08
mdh PP0654 Malate dehydrogenase −0.79 −0.52 −0.42 −0.15
Glyoxylate shunt
aceA PP4116 Isocitrate lyase −0.78 0.03 3.10 3.91
glcB PP0356 Malate synthase 0.19 0.32 0.69 0.82
  1. Carbon-limitation at high (CH) and low (CL) dilution rate, nitrogen-limitation at high (NH) and low (NL) dilution rate
  2. Boldface represents a differentiated expression pattern
  3. p value <0.05