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Patterns of indirect protein interactions suggest a spatial organization to metabolism

Perez-Bercoff, Asa; McLysaght, A; Conant, Gavin C

Description

It has long been believed that cells organize their cytoplasm so as to efficiently channel metabolites between sequential enzymes. This metabolic channeling has the potential to yield higher metabolic fluxes as well as better regulatory control over metabolism. One mechanism for achieving such channeling is to ensure that sequential enzymes in a pathway are physically close to each other in the cell. We present evidence that indirect protein interactions between related enzymes represent a...[Show more]

dc.contributor.authorPerez-Bercoff, Asa
dc.contributor.authorMcLysaght, A
dc.contributor.authorConant, Gavin C
dc.date.accessioned2015-12-07T22:44:50Z
dc.identifier.issn1742-206X
dc.identifier.urihttp://hdl.handle.net/1885/25369
dc.description.abstractIt has long been believed that cells organize their cytoplasm so as to efficiently channel metabolites between sequential enzymes. This metabolic channeling has the potential to yield higher metabolic fluxes as well as better regulatory control over metabolism. One mechanism for achieving such channeling is to ensure that sequential enzymes in a pathway are physically close to each other in the cell. We present evidence that indirect protein interactions between related enzymes represent a global mechanism for achieving metabolic channeling; the intuition being that protein interactions between enzymes and non-enzymatic mediator proteins are a powerful means of physically associating enzymes in a modular fashion. By analyzing the metabolic and protein-protein interactions networks of Escherichia coli, yeast and humans, we are able to show that all three species have many more indirect protein interactions linking enzymes that share metabolites than would be expected by chance. Moreover, these interactions are distributed non-randomly in the metabolic network. Our analyses in yeast and E. coli show that reactions possessing such interactions also show higher flux than do those lacking them. On the basis of these observations, we suggest that an important role of protein interactions with mediator proteins is to contribute to the spatial organization of the cell. This hypothesis is supported by the fact that these mediator proteins are also enriched with annotations related to signal transduction, a system where scaffolding proteins are known to limit cross-talk by controlling spatial localization. This journal is
dc.publisherRoyal Society of Chemistry
dc.sourceMolecular BioSystems
dc.subjectKeywords: Escherichia coli protein; fungal protein; mediator complex; protein; article; binding site; chemistry; Escherichia coli; human; metabolism; protein protein interaction; species difference; yeast; Binding Sites; Escherichia coli; Escherichia coli Proteins;
dc.titlePatterns of indirect protein interactions suggest a spatial organization to metabolism
dc.typeJournal article
local.description.notesImported from ARIES
local.identifier.citationvolume7
dc.date.issued2011
local.identifier.absfor060104 - Cell Metabolism
local.identifier.ariespublicationu3526593xPUB38
local.type.statusPublished Version
local.contributor.affiliationPerez-Bercoff, Asa, College of Medicine, Biology and Environment, ANU
local.contributor.affiliationMcLysaght, A, Smurfit Institute of Genetics, Trinity College,
local.contributor.affiliationConant, Gavin C, University of Missouri-Columbia
local.description.embargo2037-12-31
local.bibliographicCitation.issue11
local.bibliographicCitation.startpage3056
local.bibliographicCitation.lastpage64
local.identifier.doi10.1039/c1mb05168g
dc.date.updated2016-02-24T10:16:50Z
local.identifier.scopusID2-s2.0-80054012758
CollectionsANU Research Publications

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