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

Beckers, Veronique; Poblete-Castro, Ignacio; Tomasch, Jürgen; Wittmann, Christoph

doi:10.1186/s12934-016-0470-2

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
Gene name	Locus tag	Description	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
gltR	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
acoC	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
ppc	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

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ISSN: 1475-2859

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