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Catabolite regulation analysis of Escherichia coli for acetate overflow mechanism and co-consumption of multiple sugars based on systems biology approach using computer simulation.
J Biotechnol. 2013 Oct 20; 168(2):155-73.JB

Abstract

It is quite important to understand the basic principle embedded in the main metabolism for the interpretation of the fermentation data. For this, it may be useful to understand the regulation mechanism based on systems biology approach. In the present study, we considered the perturbation analysis together with computer simulation based on the models which include the effects of global regulators on the pathway activation for the main metabolism of Escherichia coli. Main focus is the acetate overflow metabolism and the co-fermentation of multiple carbon sources. The perturbation analysis was first made to understand the nature of the feed-forward loop formed by the activation of Pyk by FDP (F1,6BP), and the feed-back loop formed by the inhibition of Pfk by PEP in the glycolysis. Those together with the effect of transcription factor Cra caused by FDP level affected the glycolysis activity. The PTS (phosphotransferase system) acts as the feed-back system by repressing the glucose uptake rate for the increase in the glucose uptake rate. It was also shown that the increased PTS flux (or glucose consumption rate) causes PEP/PYR ratio to be decreased, and EIIA-P, Cya, cAMP-Crp decreased, where cAMP-Crp in turn repressed TCA cycle and more acetate is formed. This was further verified by the detailed computer simulation. In the case of multiple carbon sources such as glucose and xylose, it was shown that the sequential utilization of carbon sources was observed for wild type, while the co-consumption of multiple carbon sources with slow consumption rates were observed for the ptsG mutant by computer simulation, and this was verified by experiments. Moreover, the effect of a specific gene knockout such as Δpyk on the metabolic characteristics was also investigated based on the computer simulation.

Authors+Show Affiliations

Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan.No affiliation info available

Pub Type(s)

Journal Article

Language

eng

PubMed ID

23850830

Citation

Matsuoka, Yu, and Kazuyuki Shimizu. "Catabolite Regulation Analysis of Escherichia Coli for Acetate Overflow Mechanism and Co-consumption of Multiple Sugars Based On Systems Biology Approach Using Computer Simulation." Journal of Biotechnology, vol. 168, no. 2, 2013, pp. 155-73.
Matsuoka Y, Shimizu K. Catabolite regulation analysis of Escherichia coli for acetate overflow mechanism and co-consumption of multiple sugars based on systems biology approach using computer simulation. J Biotechnol. 2013;168(2):155-73.
Matsuoka, Y., & Shimizu, K. (2013). Catabolite regulation analysis of Escherichia coli for acetate overflow mechanism and co-consumption of multiple sugars based on systems biology approach using computer simulation. Journal of Biotechnology, 168(2), 155-73. https://doi.org/10.1016/j.jbiotec.2013.06.023
Matsuoka Y, Shimizu K. Catabolite Regulation Analysis of Escherichia Coli for Acetate Overflow Mechanism and Co-consumption of Multiple Sugars Based On Systems Biology Approach Using Computer Simulation. J Biotechnol. 2013 Oct 20;168(2):155-73. PubMed PMID: 23850830.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Catabolite regulation analysis of Escherichia coli for acetate overflow mechanism and co-consumption of multiple sugars based on systems biology approach using computer simulation. AU - Matsuoka,Yu, AU - Shimizu,Kazuyuki, Y1 - 2013/07/10/ PY - 2012/11/30/received PY - 2013/06/21/revised PY - 2013/06/28/accepted PY - 2013/7/16/entrez PY - 2013/7/16/pubmed PY - 2014/5/10/medline KW - 6-phosphogluconate KW - 6-phosphogluconate dehydrogenase KW - 6PG KW - Ack KW - Acs KW - CCR KW - CIT KW - CS KW - Catabolite regulation KW - Computer simulation KW - Cya KW - E4P KW - EI KW - EII KW - Eno KW - Escherichia coli KW - F6P KW - FDP KW - Fbp KW - G6P KW - G6PDH KW - GAP KW - GF6P KW - GLC KW - GOX KW - Glk KW - HPr KW - ICDH KW - ICI KW - Icl KW - MAL KW - MDH KW - MS KW - Mez KW - Modeling KW - Multiple carbon sources KW - OAA KW - PDH KW - PEP KW - PGDH KW - PP pathway KW - PTS KW - PYR KW - Pck KW - Pfk KW - Ppc KW - Pps KW - Pta KW - Pyk KW - R5P KW - RU5P KW - Rpe KW - Rpi KW - S7P KW - SUC KW - Systems biology KW - TCA cycle KW - TP KW - Tal KW - TktA KW - TktB KW - X5P KW - XT KW - XYL KW - XYLU KW - Xyi KW - Xyk KW - acetate kinase KW - acetyl coenzyme A synthetase KW - adenylate cyclase KW - carbon catabolite repression KW - citrate KW - citrate synthase KW - enolase KW - enzyme I KW - enzyme II KW - erythrose-4-phosphate KW - fructose bisphosphatase KW - fructose-1.6-bisphosphate KW - fructose-6-phosphate KW - glucokinase KW - glucose KW - glucose-6-phosphate KW - glucose-6-phosphate and fructose-6-phosphate KW - glucose-6-phosphate dehydrogenase KW - glycelaldehyde-3-phosphate KW - glyoxylate KW - histidine-phosphorylatable protein KW - isocitrate KW - isocitrate dehydrogenase KW - isocitrate lyase KW - malate KW - malate dehydrogenase KW - malate synthase KW - malic enzyme KW - oxaloacetate KW - pentose phosphate pathway KW - phosphoenol pyruvate KW - phosphoenolpyruvate carboxykinase KW - phosphoenolpyruvate carboxylase KW - phosphoenolpyruvate synthase KW - phosphofructokinase KW - phosphotransacetylase KW - phosphotransferase system KW - pyruvate KW - pyruvate dehydrogenase KW - pyruvate kinase KW - ribose phosphate isomerase KW - ribose-5-phosphate KW - ribulose phosphate epimerase KW - ribulose-5-phosphate KW - sedoheptulose-7-phosphate KW - succinate KW - transaldolase KW - transketolase I KW - transketolase II KW - tricarboxylic acid cycle KW - triose phosphate KW - xylose KW - xylose isomerase KW - xylose transport KW - xylulokinase KW - xylulose KW - xylulose-5-phosphate KW - α-ketoglutarate KW - αKG SP - 155 EP - 73 JF - Journal of biotechnology JO - J Biotechnol VL - 168 IS - 2 N2 - It is quite important to understand the basic principle embedded in the main metabolism for the interpretation of the fermentation data. For this, it may be useful to understand the regulation mechanism based on systems biology approach. In the present study, we considered the perturbation analysis together with computer simulation based on the models which include the effects of global regulators on the pathway activation for the main metabolism of Escherichia coli. Main focus is the acetate overflow metabolism and the co-fermentation of multiple carbon sources. The perturbation analysis was first made to understand the nature of the feed-forward loop formed by the activation of Pyk by FDP (F1,6BP), and the feed-back loop formed by the inhibition of Pfk by PEP in the glycolysis. Those together with the effect of transcription factor Cra caused by FDP level affected the glycolysis activity. The PTS (phosphotransferase system) acts as the feed-back system by repressing the glucose uptake rate for the increase in the glucose uptake rate. It was also shown that the increased PTS flux (or glucose consumption rate) causes PEP/PYR ratio to be decreased, and EIIA-P, Cya, cAMP-Crp decreased, where cAMP-Crp in turn repressed TCA cycle and more acetate is formed. This was further verified by the detailed computer simulation. In the case of multiple carbon sources such as glucose and xylose, it was shown that the sequential utilization of carbon sources was observed for wild type, while the co-consumption of multiple carbon sources with slow consumption rates were observed for the ptsG mutant by computer simulation, and this was verified by experiments. Moreover, the effect of a specific gene knockout such as Δpyk on the metabolic characteristics was also investigated based on the computer simulation. SN - 1873-4863 UR - https://www.unboundmedicine.com/medline/citation/23850830/Catabolite_regulation_analysis_of_Escherichia_coli_for_acetate_overflow_mechanism_and_co_consumption_of_multiple_sugars_based_on_systems_biology_approach_using_computer_simulation_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S0168-1656(13)00279-4 DB - PRIME DP - Unbound Medicine ER -