Stress induces biphasic-rewiring and modularization patterns in the metabolomic networks of Escherichia coli

M. Fayez Aziz, Philemon Chan, Johan S. Osorio, Bushra F. Minhas, Vaisak Parekatt, Gustavo Caetano-Anolles

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Metabolomic networks describe correlated change in metabolite levels that crucially link the transcriptome and proteome with the complex matter and energy dynamics of small molecule metabolism. These networks are atypical. They do not directly portray regulatory and pathway information, yet they embed both. Here we study how stress rewires the metabolomic networks of Escherichia coli. Networks with vertices describing metabolites and edges representing correlated changes in metabolite concentrations were used to study time resolved bacterial responses to four non-lethal stress perturbations, cold, heat, lactose diauxie, and oxidative stress. We find notable patterns that are common to all stress responses examined: (1) networks are random rather than scale-free, i.e. metabolite connectivity is dictated by large network components rather than 'hubs' (2) networks rewire quickly even in the absence of stress and are therefore highly dynamic; (3) rewiring occurs minutes after exposure to the Stressor and results in significant decreases in network connectivity, and (4) at longer time frames connectivity is regained. The common biphasic-rewiring pattern revealed in our time-resolved exploration of metabolite connectivity also uncovers unique structural and functional features. We find that stress-induced decreases in connectivity were always counterbalanced by increases in network modularity. Remarkably, rewiring begins with energetics and carbon metabolism that is needed for growth and then focuses on lipids, hubs and metabolic centrality needed for membrane restructuring. While these patterns may simply represent the need of the cell to stop growing and to prepare for uncertainty, the biphasic modularization of the network is an unanticipated result that links the effects of environmental perturbations and the generation of modules in biology.

Original languageEnglish (US)
Title of host publicationProceedings - 2012 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2012
Pages593-597
Number of pages5
DOIs
StatePublished - Dec 1 2012
Event2012 IEEE International Conference on Bioinformatics and Biomedicine, BIBM2012 - Philadelphia, PA, United States
Duration: Oct 4 2012Oct 7 2012

Publication series

NameProceedings - 2012 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2012

Other

Other2012 IEEE International Conference on Bioinformatics and Biomedicine, BIBM2012
CountryUnited States
CityPhiladelphia, PA
Period10/4/1210/7/12

Fingerprint

Metabolomics
Metabolites
Escherichia coli
Metabolism
Proteome
Lactose
Transcriptome
Uncertainty
Oxidative Stress
Carbon
Hot Temperature
Network components
Time and motion study
Oxidative stress
Lipids
Membranes
Growth
Proteins
Molecules

Keywords

  • Dynamic behavior
  • environmental perturbation
  • metabolism
  • metabolite
  • metabolomics
  • module
  • network connectivity
  • random networks

ASJC Scopus subject areas

  • Biomedical Engineering
  • Health Informatics

Cite this

Aziz, M. F., Chan, P., Osorio, J. S., Minhas, B. F., Parekatt, V., & Caetano-Anolles, G. (2012). Stress induces biphasic-rewiring and modularization patterns in the metabolomic networks of Escherichia coli. In Proceedings - 2012 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2012 (pp. 593-597). [6392626] (Proceedings - 2012 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2012). https://doi.org/10.1109/BIBM.2012.6392626

Stress induces biphasic-rewiring and modularization patterns in the metabolomic networks of Escherichia coli. / Aziz, M. Fayez; Chan, Philemon; Osorio, Johan S.; Minhas, Bushra F.; Parekatt, Vaisak; Caetano-Anolles, Gustavo.

Proceedings - 2012 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2012. 2012. p. 593-597 6392626 (Proceedings - 2012 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2012).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Aziz, MF, Chan, P, Osorio, JS, Minhas, BF, Parekatt, V & Caetano-Anolles, G 2012, Stress induces biphasic-rewiring and modularization patterns in the metabolomic networks of Escherichia coli. in Proceedings - 2012 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2012., 6392626, Proceedings - 2012 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2012, pp. 593-597, 2012 IEEE International Conference on Bioinformatics and Biomedicine, BIBM2012, Philadelphia, PA, United States, 10/4/12. https://doi.org/10.1109/BIBM.2012.6392626
Aziz MF, Chan P, Osorio JS, Minhas BF, Parekatt V, Caetano-Anolles G. Stress induces biphasic-rewiring and modularization patterns in the metabolomic networks of Escherichia coli. In Proceedings - 2012 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2012. 2012. p. 593-597. 6392626. (Proceedings - 2012 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2012). https://doi.org/10.1109/BIBM.2012.6392626
Aziz, M. Fayez ; Chan, Philemon ; Osorio, Johan S. ; Minhas, Bushra F. ; Parekatt, Vaisak ; Caetano-Anolles, Gustavo. / Stress induces biphasic-rewiring and modularization patterns in the metabolomic networks of Escherichia coli. Proceedings - 2012 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2012. 2012. pp. 593-597 (Proceedings - 2012 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2012).
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