Dynamic network topology changes in functional modules predict responses to oxidative stress in yeast

Peddinti Gopalacharyulu, Vidya Velagapudi, Erno Lindfors, Halperin Eran, Matej Orešič (Corresponding Author)

Research output: Contribution to journalArticleScientificpeer-review

11 Citations (Scopus)

Abstract

In response to environmental challenges, biological systems respond with dynamic adaptive changes in order to maintain the functionality of the system. Such adaptations may lead to cumulative stress over time, possibly leading to global failure of the system. When studying such systems responses, it is therefore important to understand them in system-wide and dynamic context. Here we hypothesize that dynamic changes in the topology of functional modules of integrated biological networks reflect their activity under specific environmental challenges. We introduce topological enrichment analysis of functional subnetworks (TEAFS), a method for the analysis of integrated molecular profile and interactome data, which we validated by comprehensive metabolomic analysis of dynamic yeast response under oxidative stress. TEAFS identified activation of multiple stress response related mechanisms, such as lipid metabolism and phospholipid biosynthesis. We identified, among others, a fatty acid elongase IFA38 as a hub protein which was absent at all time points under oxidative stress conditions. The deletion mutant of the IFA38 encoding gene is known for the accumulation of ceramides. By applying a comprehensive metabolomic analysis, we confirmed the increased concentrations over time of ceramides and palmitic acid, a precursor of de novoceramide biosynthesis. Our results imply that the connectivity of the system is being dynamically modulated in response to oxidative stress, progressively leading to the accumulation of (lipo)toxic lipids such as ceramides. Studies of local network topology dynamics can be used to investigate as well as predict the activity of biological processes and the system’s responses to environmental challenges and interventions.
Original languageEnglish
Pages (from-to)276-287
JournalMolecular bioSystems
Volume5
DOIs
Publication statusPublished - 2009
MoE publication typeA1 Journal article-refereed

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Ceramides
Oxidative Stress
Metabolomics
Yeasts
Biological Phenomena
Palmitic Acid
Poisons
Lipid Metabolism
Phospholipids
Lipids
Genes
Proteins

Cite this

Gopalacharyulu, Peddinti ; Velagapudi, Vidya ; Lindfors, Erno ; Eran, Halperin ; Orešič, Matej. / Dynamic network topology changes in functional modules predict responses to oxidative stress in yeast. In: Molecular bioSystems. 2009 ; Vol. 5. pp. 276-287.
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abstract = "In response to environmental challenges, biological systems respond with dynamic adaptive changes in order to maintain the functionality of the system. Such adaptations may lead to cumulative stress over time, possibly leading to global failure of the system. When studying such systems responses, it is therefore important to understand them in system-wide and dynamic context. Here we hypothesize that dynamic changes in the topology of functional modules of integrated biological networks reflect their activity under specific environmental challenges. We introduce topological enrichment analysis of functional subnetworks (TEAFS), a method for the analysis of integrated molecular profile and interactome data, which we validated by comprehensive metabolomic analysis of dynamic yeast response under oxidative stress. TEAFS identified activation of multiple stress response related mechanisms, such as lipid metabolism and phospholipid biosynthesis. We identified, among others, a fatty acid elongase IFA38 as a hub protein which was absent at all time points under oxidative stress conditions. The deletion mutant of the IFA38 encoding gene is known for the accumulation of ceramides. By applying a comprehensive metabolomic analysis, we confirmed the increased concentrations over time of ceramides and palmitic acid, a precursor of de novoceramide biosynthesis. Our results imply that the connectivity of the system is being dynamically modulated in response to oxidative stress, progressively leading to the accumulation of (lipo)toxic lipids such as ceramides. Studies of local network topology dynamics can be used to investigate as well as predict the activity of biological processes and the system’s responses to environmental challenges and interventions.",
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Gopalacharyulu, P, Velagapudi, V, Lindfors, E, Eran, H & Orešič, M 2009, 'Dynamic network topology changes in functional modules predict responses to oxidative stress in yeast', Molecular bioSystems, vol. 5, pp. 276-287. https://doi.org/10.1039/b815347g

Dynamic network topology changes in functional modules predict responses to oxidative stress in yeast. / Gopalacharyulu, Peddinti; Velagapudi, Vidya; Lindfors, Erno; Eran, Halperin; Orešič, Matej (Corresponding Author).

In: Molecular bioSystems, Vol. 5, 2009, p. 276-287.

Research output: Contribution to journalArticleScientificpeer-review

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