Table 5.

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

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

Carbon-limitation at high (CH) and low (CL) dilution rate, nitrogen-limitation at high (NH) and low (NL) dilution rate

Boldface represents a differentiated expression pattern

p value <0.05