Horizontal and vertical growth of S. cerevisiae metabolic network.

Handle URI:
http://hdl.handle.net/10754/596789
Title:
Horizontal and vertical growth of S. cerevisiae metabolic network.
Authors:
Grassi, Luigi; Tramontano, Anna
Abstract:
BACKGROUND: The growth and development of a biological organism is reflected by its metabolic network, the evolution of which relies on the essential gene duplication mechanism. There are two current views about the evolution of metabolic networks. The retrograde model hypothesizes that a pathway evolves by recruiting novel enzymes in a direction opposite to the metabolic flow. The patchwork model is instead based on the assumption that the evolution is based on the exploitation of broad-specificity enzymes capable of catalysing a variety of metabolic reactions. RESULTS: We analysed a well-studied unicellular eukaryotic organism, S. cerevisiae, and studied the effect of the removal of paralogous gene products on its metabolic network. Our results, obtained using different paralog and network definitions, show that, after an initial period when gene duplication was indeed instrumental in expanding the metabolic space, the latter reached an equilibrium and subsequent gene duplications were used as a source of more specialized enzymes rather than as a source of novel reactions. We also show that the switch between the two evolutionary strategies in S. cerevisiae can be dated to about 350 million years ago. CONCLUSIONS: Our data, obtained through a novel analysis methodology, strongly supports the hypothesis that the patchwork model better explains the more recent evolution of the S. cerevisiae metabolic network. Interestingly, the effects of a patchwork strategy acting before the Euascomycete-Hemiascomycete divergence are still detectable today.
Citation:
Grassi L, Tramontano A (2011) Horizontal and vertical growth of S. cerevisiae metabolic network. BMC Evolutionary Biology 11: 301. Available: http://dx.doi.org/10.1186/1471-2148-11-301.
Publisher:
Springer Nature
Journal:
BMC Evolutionary Biology
KAUST Grant Number:
KUK-I1-012-43
Issue Date:
14-Oct-2011
DOI:
10.1186/1471-2148-11-301
PubMed ID:
21999464
PubMed Central ID:
PMC3216907
Type:
Article
ISSN:
1471-2148
Sponsors:
This work was partially supported by Award No. KUK-I1-012-43 made by King Abdullah University of Science and Technology (KAUST), by Fondazione Roma and by the Italian Ministry of Health, contract no.onc_ord 25/07, FIRB ITALBIONET and PROTEOMICA.
Appears in Collections:
Publications Acknowledging KAUST Support

Full metadata record

DC FieldValue Language
dc.contributor.authorGrassi, Luigien
dc.contributor.authorTramontano, Annaen
dc.date.accessioned2016-02-21T08:50:43Zen
dc.date.available2016-02-21T08:50:43Zen
dc.date.issued2011-10-14en
dc.identifier.citationGrassi L, Tramontano A (2011) Horizontal and vertical growth of S. cerevisiae metabolic network. BMC Evolutionary Biology 11: 301. Available: http://dx.doi.org/10.1186/1471-2148-11-301.en
dc.identifier.issn1471-2148en
dc.identifier.pmid21999464en
dc.identifier.doi10.1186/1471-2148-11-301en
dc.identifier.urihttp://hdl.handle.net/10754/596789en
dc.description.abstractBACKGROUND: The growth and development of a biological organism is reflected by its metabolic network, the evolution of which relies on the essential gene duplication mechanism. There are two current views about the evolution of metabolic networks. The retrograde model hypothesizes that a pathway evolves by recruiting novel enzymes in a direction opposite to the metabolic flow. The patchwork model is instead based on the assumption that the evolution is based on the exploitation of broad-specificity enzymes capable of catalysing a variety of metabolic reactions. RESULTS: We analysed a well-studied unicellular eukaryotic organism, S. cerevisiae, and studied the effect of the removal of paralogous gene products on its metabolic network. Our results, obtained using different paralog and network definitions, show that, after an initial period when gene duplication was indeed instrumental in expanding the metabolic space, the latter reached an equilibrium and subsequent gene duplications were used as a source of more specialized enzymes rather than as a source of novel reactions. We also show that the switch between the two evolutionary strategies in S. cerevisiae can be dated to about 350 million years ago. CONCLUSIONS: Our data, obtained through a novel analysis methodology, strongly supports the hypothesis that the patchwork model better explains the more recent evolution of the S. cerevisiae metabolic network. Interestingly, the effects of a patchwork strategy acting before the Euascomycete-Hemiascomycete divergence are still detectable today.en
dc.description.sponsorshipThis work was partially supported by Award No. KUK-I1-012-43 made by King Abdullah University of Science and Technology (KAUST), by Fondazione Roma and by the Italian Ministry of Health, contract no.onc_ord 25/07, FIRB ITALBIONET and PROTEOMICA.en
dc.publisherSpringer Natureen
dc.rightsThis is an Open Access article distributed under the terms of the Creative Commons Attribution License (), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.en
dc.rights.urihttp://creativecommons.org/licenses/by/2.0en
dc.subject.meshEvolution, Molecularen
dc.subject.meshMetabolic Networks and Pathwaysen
dc.titleHorizontal and vertical growth of S. cerevisiae metabolic network.en
dc.typeArticleen
dc.identifier.journalBMC Evolutionary Biologyen
dc.identifier.pmcidPMC3216907en
dc.contributor.institutionUniversita degli Studi di Roma La Sapienza, Rome, Italyen
dc.contributor.institutionUniversita degli Studi di Roma La Sapienza, Rome, Italyen
kaust.grant.numberKUK-I1-012-43en

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