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Comparison of dynamic responses of cellular metabolites in Escherichia coli to pulse addition of substrates

  • Section Cellular and Molecular Biology
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Abstract

We conducted an integrated study of cell growth parameters, product formation, and the dynamics of intracellular metabolite concentrations using Escherichia coli with genes knocked out in the glycolytic and oxidative pentose phosphate pathway (PPP) for glucose catabolism. We investigated the same characteristics in the wild-type strain, using acetate or pyruvate as the sole carbon source. Dramatic effects on growth parameters and extracellular and intracellular metabolite concentrations were observed after blocking either glycolytic breakdown of glucose by inactivation of phosphoglucose isomerase (disruption of pgi gene) or pentose phosphate breakdown of glucose by inactivation of glucose-6-phosphate dehydrogenase (disruption of zwf gene). Reducing power (NADPH) was mainly produced through PPP when the pgi gene was knocked out, while NADPH was produced through the tricarboxylic acid (TCA) cycle by isocitrate dehydrogenase or NADP-linked malic enzyme when the zwf gene was knocked out. As expected, when the pgi gene was knocked out, intracellular concentrations of PPP metabolites were high and glycolytic and concentrations of TCA cycle pathway metabolites were low. In the zwf gene knockout, concentrations of PPP metabolites were low and concentrations of intracellular glycolytic and TCA cycle metabolites were high.

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Abbreviations

CER:

CO2 evolution rate

DCW:

dry cell weight

ED:

Entner-Doudoroff

EMP:

Embden-Mayerhof-Paranas

MEZ:

malic enzyme

OD:

optical density

OUR:

oxygen uptake rate

PGI:

phosphoglucose isomerase

PPP:

pentose phosphate pathway

TCA:

tricarboxylic acid

Yx/s :

cell mass yield

6PGDH:

6-phosphogluconate dehydrogenase

Eda:

Entner-Douderoff aldolase

Edd:

Entner-Douderoff dehydralase

Eno:

enolase

Fba:

fructose-1,6-bisphosphate aldolase

G6PDH:

glucose-6-phosphate dehydrogenase

GAPDH:

glyceraldehyde-3-phosphate dehydrogenase

GDH:

glutamate dehydrogenase

Hxk:

hexokinase

ICDH:

isocitrate dehydrogenase

LDH:

lactate dehydrogenase

MDH:

malate dehydrogenase

Mk:

myokinase

Pck:

PEP carboxykinase

Pgi:

phosphoglucose isomerase

Ppc:

phosphoenolpyruvate carboxylase

Pta:

phosphotransacetylase

PTS:

phosphotransferase system

Pyk:

pyruvate kinase

Rpe:

ribose-phosphate epimerase

Rpi:

ribose-phosphate isomerase

Tkt:

transketolase

Tpi:

triosephosphate isomerase

Tal:

transaldolase

2PG:

2-phosphoglycerate

6PG:

6-phosphogluconate

AcCoA:

acetyl-coenzyme A

ADP:

adenosine diphosphate

AKG:

α-ketoglutarate

AMP:

adenosine monophosphate

ATP:

adenosine triphosphate

DHAP:

dihydroxyacetone phosphate

E4P:

erythrose-4-phosphate

F6P:

fructose-6-phosphate

FBP:

fructose-1,6-bisphosphate

G6P:

glucose-6-phosphate

GAP:

glyceraldehyde-3-phosphate

ICT:

isocitrate

NAD:

diphosphopyridindinucleotide, oxidized

NADH:

diphosphopyridindinucleotide, reduced

NADP:

diphosphopyridindinucleotide-phosphate, oxidized

NADPH:

diphosphopyridindinucleotide-phosphate, reduced

OAA:

oxaloacetate

PEP:

phosphoenolpyruvate

PYR:

pyruvate

R5P:

ribose-5-phosphate

RU5P:

ribulose-5-phosphate

SUC:

succinate

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Authors and Affiliations

  1. Centre of Research in Computational Sciences and Informatics in Biology, Biodiversity, Environment, Agriculture and Healthcare (CRYSTAL), Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, 50603, Malaysia

    Md. Aminul Hoque, Atefeh Taherian Fard & Amir Feisal Merican

  2. Division of Information Science and Biostatistics, Department of Medical Informatics, Niigata University Medical and Dental Hospital, Asahimachi-dori 1-754, Niigata, Japan

    Md. Aminul Hoque & Kohei Akazawa

  3. Faculty of Science, Rajshahi University, Rajshahi, 6205, Bangladesh

    Md. Aminul Hoque & Mosfequr Rahman

  4. Centre of Excellence in Biotechnology Research, King Saud University, Riyadh, 11451, Kingdom of Saudi Arabia

    Omar Alattas

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  1. Md. Aminul Hoque
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  2. Atefeh Taherian Fard
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  3. Mosfequr Rahman
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  4. Omar Alattas
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Correspondence to Md. Aminul Hoque.

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Hoque, M.A., Fard, A.T., Rahman, M. et al. Comparison of dynamic responses of cellular metabolites in Escherichia coli to pulse addition of substrates. Biologia 66, 954–966 (2011). https://doi.org/10.2478/s11756-011-0136-9

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  • DOI: https://doi.org/10.2478/s11756-011-0136-9

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