Physiological and Molecular Timing of the Glucose to Acetate Transition in Escherichia coli
Abstract
:1. Introduction
2. Results and Discussion
2.1. Results
2.1.1. Macrophenotype Parameters of the Glucose/Acetate Transition in a Model Condition
2.1.2. Changes in Metabolite Profiles
2.1.3. Changes in Gene Expression during the Glucose-Acetate Transition
2.1.4. Expression of Key Metabolic Genes during the Glucose-Acetate Transition
2.1.5. Data Integration
2.2. Discussion
3. Experimental Section
3.1. Strain, Media and Growth Conditions
3.2. Metabolome Analysis
3.3. Transcriptome Analysis
3.4. RT-PCR Analysis
Name | Sequence (5' to 3') | Name | Sequence (5' to 3') |
---|---|---|---|
Q-16S-3' | ATCCGGACTACGACGCACTT | Q-lacZ3' | GCATAACCACCACGCTCATCG |
Q-16S-5' | ACGACCAGGGCTACACACG | Q-lacZ5' | ACCTACGGGTAACAGTTTCTTTATG |
Q-AceA-3' | AACCAGCAGGGTTGGAACG | Q-maeA3' | ATTGCGCGGGAGACTTTCTG |
Q-AceA-5' | ACATGGGCGGCAAAGTTTTA | Q-maeA5' | AAGTGAAACGCTGGCGCAGT |
Q-aceB-3' | TCAGGCCATAAATCGGCACA | Q-mdh3' | TGGCCCATAGACAGGGTTGC |
Q-aceB-5' | GGTGAACGCACCGAAGAAGG | Q-mdh5' | CCGAGCAGGAAGTGGCTGAT |
Q-acs-3' | GGATCTTCGGCGTTCATCTC | Q-pck3' | GTGTCTACGCCCGGCAGTTC |
Q-acs-5' | GGGAAAATTGACTGGCAGGA | Q-pck5' | GACGCCATCCTCAACGGTTC |
Q-crp3' | ACAGGCCCAGTTCGCCAATA | Q-pfkA3' | CACCCATGTAGGAACCGTCA |
Q-crp5' | AGGCTCTGTGGCAGTGCTGA | Q-pfkA5' | AATTCCGCGACGAGAACATC |
Q-cya3' | CCCGGCGGCACATAAATAAA | Q-ppc3' | CAGGCGAGAACGCAGGTTTT |
Q-cya5' | GCCGCGTTTGAAGCATTACC | Q-ppc5' | ATGGTTGAAGCGACCCCTGA |
Q-edd3' | ACCAAGTGGCGGCATGAGTT | Q-pps3' | CTGGCTCGTAACGCTCACCA |
Q-edd5' | GTTTGCTGGACCGCGATTGT | Q-pps5' | GTGCCGCGTTTTATCCGAAG |
Q-frdD3' | CCGCAGGTACGTGGATTTTC | Q-ptsG3' | GGAATGTCGCCGTGGAAAAC |
Q-frdD5' | TGGTCGCGTATTCCTGTTCC | Q-ptsG5' | CCGTTTGGTCTGCACCACAT |
Q-glgS3' | GCTCTCTTGCCTGCATCATCTG | Q-pykF3' | GCAACCATGATGCCGTCAGA |
Q-glgS5' | CGGTCGATATTCTGGCCGTTA | Q-pykF5' | CGGCGAAAACATCCACATCA |
Q-Icd-3' | TTCGTCACCGATGTTTGCAC | Q-sdhD3' | ACACACCCCACACCACAACG |
Q-Icd-5' | CGCCTGTATGAACCTGAACG | Q-sdhD5' | CGTTAAACCGCTGGCTTTGC |
Q-ihfA3' | TACTCGTCTTTGGGCGAAGC | Q-sucA3' | GGTGTCAGGGTCGGAGATCG |
Q-ihfA5' | GCGAGGATATTCCCATTACAGC | Q-sucA5' | ACGGGAGTCAAACCGGATCA |
Q-ihfB-3' | CAAAGAGAAACTGCCGAAACC | Q-yfiA3' | TGTGGCGTCAGCAACAAACC |
Q-ihfB-5' | GCCAAGACGGTTGAAGATGC | Q-yfiA5' | ACCGTCTCGCCAAACTGGAA |
Q-infA3' | ACAATGCGGCCTTTGCTCAG | Q-zwf3' | GCCCTTCGATCCCCACTTCT |
Q-infA5' | GCACACATCTCCGGTAAAATGC | Q-zwf5' | GGCGCTGCGTTTTGCTAACT |
4. Conclusions
Abbreviations
1,3DPG | 1,3-bisphospho-D-glycerate |
2/3PG | 2-/3-phosphoglycerate |
6PG | 6-phospho D-gluconate |
6-PG | 6-phosphogluconate |
6PGL | 6-phospho D-glucono-1,5-lactone |
a-KG | 2-oxoglutarate |
AC | acetate |
acea | isocitrate lyase |
aceb | malate synthase |
aceef | pyruvate dehydrogenase |
ack | acetate kinase |
acn | aconitate hydratase |
ACoA | acetyl-CoA |
ACP | acetyl phosphate |
acs | acetyl-CoA synthetase |
AMP | adenosine-monophosphate |
ADP | adenosine-diphosphate |
ATP | adenosine-triphosphate |
CACN | cis-aconitate |
CIT | citrate |
crp | CRP transcriptional dual regulator |
cya | adenylate cyclase |
DHAP | dihydroxyacetone phosphate |
E4P | erythrose-4-phosphate |
ED | Entner-Doudoroff |
eno | enolase |
F6P | fructose-6-phosphate |
fba | fructose bisphosphate aldolase |
FBP | fructose-bisphosphate |
Fbp | fructose-1,6-bisphosphatase |
FOR | formate |
frd | fumarate reductase |
fum | fumarase |
FUM | fumarate |
G6P | glucose-6-phosphate |
gap | glyceraldehyde 3-phosphate dehydrogenase |
GHAP | D-glyceraldehyde 3-phosphate |
GLC | glucose |
GLX | glyoxylate |
GLYC | glycolysis |
gltA | citrate synthase |
GMP | guanosine-monophosphate |
GDP | guanosine-diphosphate |
GTP | guanosine-triphosphate |
gnd | 6-phosphogluconate dehydrogenase |
gpm | 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase |
IC | ionic chromatography |
icd | isocitrate dehydrogenase |
ICIT | iso-citrate |
mae | malate dehydrogenase |
MAL | malate |
mdh | malate dehydrogenase |
MS | mass spectrometry |
NAD+ | beta-nicotinamide adenine dinucleotide |
NMR | nuclear magnetic resonance |
OA | oxaloacetate |
pck | phosphoenolpyruvate carboxykinase |
PEP | phosphoenolpyruvate |
Pfk | 6-phosphofructokinase |
pfl | pyruvate formate-lyase |
pgi | phosphoglucose isomerase |
pgk | phosphoglycerate kinase |
pgl | 6-phosphogluconolactonase |
PP | pentose phosphate |
ppc | phosphoenolpyruvate carboxylase |
PPP | pentose phosphate pathway |
pps | phosphoenolpyruvate synthetase |
pta | phosphate acetyltransferase |
PTS | phosphotransferase system |
pyk | pyruvate kinase |
PYR | pyruvate |
R5P | D-ribose 5-phosphate |
Rib-5P | ribose-5-phosphate |
rpe | ribulose-5-phosphate 3-epimerase |
rpi | ribose-5-phosphate isomerase |
RT-PCR | reverse transcription polymerase chain reaction |
RU5P | D-ribulose 5-phosphate |
S7P | D-sedoheptulose 7-phosphate |
sdh | succinate dehydrogenase |
suc | 2-oxoglutarate decarboxylase |
SUC | succinate |
Succ | succinyl-CoA synthetase |
SUCCoA | succinyl-CoA |
tal | transaldolase |
TCA | Tricarboxylic acid |
tkt | transketolase |
tpi | triose phosphate isomerase |
UMP | uridine-monophosphate |
UDP | uridine-diphosphate |
UTP | uridine-triphosphate |
XUP | D-xylulose 5-phosphate |
zwf | glucose 6-phosphate-1-dehydrogenase |
Acknowledgments
Conflicts of Interest
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Enjalbert, B.; Letisse, F.; Portais, J.-C. Physiological and Molecular Timing of the Glucose to Acetate Transition in Escherichia coli. Metabolites 2013, 3, 820-837. https://doi.org/10.3390/metabo3030820
Enjalbert B, Letisse F, Portais J-C. Physiological and Molecular Timing of the Glucose to Acetate Transition in Escherichia coli. Metabolites. 2013; 3(3):820-837. https://doi.org/10.3390/metabo3030820
Chicago/Turabian StyleEnjalbert, Brice, Fabien Letisse, and Jean-Charles Portais. 2013. "Physiological and Molecular Timing of the Glucose to Acetate Transition in Escherichia coli" Metabolites 3, no. 3: 820-837. https://doi.org/10.3390/metabo3030820