Abstract
Many regulatory processes in the cell are based on the control of gene expression through the interaction of transcription factors. However, enzymatic regulation often overlays transcriptional regulation and even, in some metabolic pathways, enzymatic regulation prevails. The present study addresses the regulatory network of Escherichia coli and offers a global view of the regulation of its metabolic pathways. It identifies the regulatory mechanisms responsible for key metabolic activities and details the structures behind such mechanisms. This knowledge is considered of relevance to further studies on the bacteria’s system and its industrial application, namely for understanding the signal cascades comprised in the responses to various environmental stresses.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Thiele, I., Jamshidi, N., Fleming, R.M., Palsson, B.O.: Genome-scale reconstruction of Escherichia coli’s transcriptional and translational machinery: a knowledge base, its mathematical formulation, and its functional characterization. PLoS Comput. Biol. 5, e1000312 (2009)
Abdul Kadir, T.A., Mannan, A.A., Kierzek, A.M., McFadden, J., Shimizu, K.: Modeling and simulation of the main metabolism in Escherichia coli and its several single-gene knockout mutants with experimental verification. Microb. Cell Fact. 9, 88 (2010)
Feist, A.M., Palsson, B.O.: The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli. Nat. Biotechnol. 26, 659–667 (2008)
Feist, A.M., Henry, C.S., Reed, J.L., Krummenacker, M., Joyce, A.R., Karp, P.D., Broadbelt, L.J., Hatzimanikatis, V., Palsson, B.O.: A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Mol. Syst. Biol. 3, 121 (2007)
Keseler, I.M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A.G., Mackie, A., Paulsen, I., Gunsalus, R.P., Karp, P.D.: EcoCyc: a comprehensive database of Escherichia coli biology. Nucleic Acids Res. (2010)
Shen-Orr, S.S., Milo, R., Mangan, S., Alon, U.: Network motifs in the transcriptional regulation network of Escherichia coli. Nat. Genet. 31, 64–68 (2002)
Alon, U.: Network motifs: theory and experimental approaches. Nat. Rev. Genet. 8, 450–461 (2007)
Hu, P., Janga, S.C., Babu, M., Diaz-Mejia, J.J., Butland, G., Yang, W., Pogoutse, O., Guo, X., Phanse, S., Wong, P., Chandran, S., Christopoulos, C., Nazarians-Armavil, A., Nasseri, N.K., Musso, G., Ali, M., Nazemof, N., Eroukova, V., Golshani, A., Paccanaro, A., Greenblatt, J.F., Moreno-Hagelsieb, G., Emili, A.: Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 7, e96 (2009)
Ma, H.W., Zhao, X.M., Yuan, Y.J., Zeng, A.P.: Decomposition of metabolic network into functional modules based on the global connectivity structure of reaction graph. Bioinformatics 20, 1870–1876 (2004)
Shen-Orr, S.S., Milo, R., Mangan, S., Alon, U.: Network motifs in the transcriptional regulation network of Escherichia coli. Nat. Genet. 31, 64–68 (2002)
Shalel-Levanon, S., San, K.Y., Bennett, G.N.: Effect of oxygen, and ArcA and FNR regulators on the expression of genes related to the electron transfer chain and the TCA cycle in Escherichia coli. Metab. Eng. 7, 364–374 (2005)
Brondijk, T.H., Nilavongse, A., Filenko, N., Richardson, D.J., Cole, J.A.: NapGH components of the periplasmic nitrate reductase of Escherichia coli K-12: location, topology and physiological roles in quinol oxidation and redox balancing. Biochem. J. 379, 47–55 (2004)
van Wonderen, J.H., Burlat, B., Richardson, D.J., Cheesman, M.R., Butt, J.N.: The nitric oxide reductase activity of cytochrome c nitrite reductase from Escherichia coli. J. Biol. Chem. 283, 9587–9594 (2008)
Castanie-Cornet, M.P., Cam, K., Bastiat, B., Cros, A., Bordes, P., Gutierrez, C.: Acid stress response in Escherichia coli: mechanism of regulation of gadA transcription by RcsB and GadE. Nucleic Acids Res. 38, 3546–3554 (2010)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2011 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Lourenço, A., Carneiro, S., Pinto, J.P., Rocha, M., Ferreira, E.C., Rocha, I. (2011). Interpreting the Regulatory Interplay in E. coli Metabolic Pathways. In: Rocha, M.P., Rodríguez, J.M.C., Fdez-Riverola, F., Valencia, A. (eds) 5th International Conference on Practical Applications of Computational Biology & Bioinformatics (PACBB 2011). Advances in Intelligent and Soft Computing, vol 93. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-19914-1_40
Download citation
DOI: https://doi.org/10.1007/978-3-642-19914-1_40
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-19913-4
Online ISBN: 978-3-642-19914-1
eBook Packages: EngineeringEngineering (R0)