Metabolic regulation of an fnr gene knockout Escherichia coli under oxygen limitation.
In addition to our previous study on the effect of fnr gene knockout on the metabolism in Escherichia coli under aerobic conditions (Kumar and Shimizu, Microb Cell Fact 2011), here we further investigated the effect of fnr gene knockout on the metabolism under micro-aerobic condition based on gene expressions, enzyme activities and intracellular metabolic fluxes. The objective of the present research is to clarify the metabolic regulation mechanism on how the culture environment, such as oxygen level, affects the cell metabolism in relation to gene expressions, enzyme activities and fluxes via global regulators such as Fnr and ArcA/B systems. Under micro-aerobic condition, the flux through Pfl and Frd were reduced for the mutant, which are due to fnr gene knockout. The decreased flux through Pfl may have caused accumulation of PYR, which increased the flux through LDH. The fnr gene knockout caused arcA to be downregulated, and thus the TCA cycle was activated, and cyoA and cydB genes were upregulated. The downregulation of arcA caused lpdA and aceE, F to be upregulated where the flux through PDHc increased. The fnr gene knockout indirectly caused cra gene transcript level to be decreased, which in turn caused the glycolysis genes to be upregulated, which correspond to the increase in the specific glucose consumption rate. The fnr gene knockout also caused crp transcript level to be increased, where there might be some relationship between the two due to similar structure and gene sequence. It may be quite important to understand the metabolic regulation mechanism based on different levels of information for the efficient metabolic engineering and control of the culture environment for process optimization.
Kyushu Institute of Technology, Department of Bioscience & Bioinformatics, Iizuka, Fukuoka, Japan.
Lolo Wal
LW
Marzan
Khandaker Al Zaid
KA
Siddiquee
Kazuyuki
K
Shimizu
D000693:Anaerobiosis; D001425:Bacterial Outer Membrane Proteins / Q000235:genetics / Q000378:metabolism; D002952:Citric Acid Cycle / Q000235:genetics; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000235:genetics*; D015964:Gene Expression Regulation, Bacterial; D055786:Gene Knockout Techniques; D005947:Glucose / Q000378:metabolism; D006019:Glycolysis / Q000235:genetics; D007218:Industrial Microbiology / Q000379:methods*; D007506:Iron-Sulfur Proteins / Q000172:deficiency / Q000235:genetics*; D060847:Metabolic Engineering / Q000379:methods*; D010100:Oxygen / Q000378:metabolism; D012333:RNA, Messenger / Q000032:analysis / Q000096:biosynthesis; D012097:Repressor Proteins / Q000235:genetics / Q000378:metabolism
D001425:Bacterial Outer Membrane Proteins; D029968:Escherichia coli Proteins; C060704:FNR protein, E coli; D007506:Iron-Sulfur Proteins; D012333:RNA, Messenger; D012097:Repressor Proteins; D005947:Glucose; D010100:Oxygen