Characterizing selective pressures on the pathway for de novo biosynthesis of pyrimidines in yeast

Persistent Link:
http://hdl.handle.net/10150/610280
Title:
Characterizing selective pressures on the pathway for de novo biosynthesis of pyrimidines in yeast
Author:
Hermansen, Russell A.; Mannakee, Brian K.; Knecht, Wolfgang; Liberles, David A.; Gutenkunst, Ryan N.
Affiliation:
Department of Molecular Biology, University of Wyoming; Department of Biology and Center for Computational Genetics and Genomics, Temple University; Division of Epidemiology and Biostatistics, Mel and Enid Zuckerman College of Public Health, University of Arizona; Department of Biology and Lund Protein Production Platform, Lund University; Department of Molecular and Cellular Biology, University of Arizona
Issue Date:
2015
Publisher:
BioMed Central Ltd
Citation:
Hermansen et al. BMC Evolutionary Biology (2015) 15:232 DOI 10.1186/s12862-015-0515-x
Journal:
BMC Evolutionary Biology
Rights:
© 2015 Hermansen et al. Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/)
Collection Information:
This item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at repository@u.library.arizona.edu.
Abstract:
BACKGROUND: Selection on proteins is typically measured with the assumption that each protein acts independently. However, selection more likely acts at higher levels of biological organization, requiring an integrative view of protein function. Here, we built a kinetic model for de novo pyrimidine biosynthesis in the yeast Saccharomyces cerevisiae to relate pathway function to selective pressures on individual protein-encoding genes. RESULTS: Gene families across yeast were constructed for each member of the pathway and the ratio of nonsynonymous to synonymous nucleotide substitution rates (dN/dS) was estimated for each enzyme from S. cerevisiae and closely related species. We found a positive relationship between the influence that each enzyme has on pathway function and its selective constraint. CONCLUSIONS: We expect this trend to be locally present for enzymes that have pathway control, but over longer evolutionary timescales we expect that mutation-selection balance may change the enzymes that have pathway control.
EISSN:
1471-2148
DOI:
10.1186/s12862-015-0515-x
Keywords:
Evolutionary systems biology; Metabolic pathway evolution; Phylogenetics; Kinetic model; Enzyme evolution; Substitution rate
Version:
Final published version
Additional Links:
http://www.biomedcentral.com/1471-2148/15/232

Full metadata record

DC FieldValue Language
dc.contributor.authorHermansen, Russell A.en
dc.contributor.authorMannakee, Brian K.en
dc.contributor.authorKnecht, Wolfgangen
dc.contributor.authorLiberles, David A.en
dc.contributor.authorGutenkunst, Ryan N.en
dc.date.accessioned2016-05-20T09:03:04Z-
dc.date.available2016-05-20T09:03:04Z-
dc.date.issued2015en
dc.identifier.citationHermansen et al. BMC Evolutionary Biology (2015) 15:232 DOI 10.1186/s12862-015-0515-xen
dc.identifier.doi10.1186/s12862-015-0515-xen
dc.identifier.urihttp://hdl.handle.net/10150/610280-
dc.description.abstractBACKGROUND: Selection on proteins is typically measured with the assumption that each protein acts independently. However, selection more likely acts at higher levels of biological organization, requiring an integrative view of protein function. Here, we built a kinetic model for de novo pyrimidine biosynthesis in the yeast Saccharomyces cerevisiae to relate pathway function to selective pressures on individual protein-encoding genes. RESULTS: Gene families across yeast were constructed for each member of the pathway and the ratio of nonsynonymous to synonymous nucleotide substitution rates (dN/dS) was estimated for each enzyme from S. cerevisiae and closely related species. We found a positive relationship between the influence that each enzyme has on pathway function and its selective constraint. CONCLUSIONS: We expect this trend to be locally present for enzymes that have pathway control, but over longer evolutionary timescales we expect that mutation-selection balance may change the enzymes that have pathway control.en
dc.language.isoenen
dc.publisherBioMed Central Ltden
dc.relation.urlhttp://www.biomedcentral.com/1471-2148/15/232en
dc.rights© 2015 Hermansen et al. Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/)en
dc.subjectEvolutionary systems biologyen
dc.subjectMetabolic pathway evolutionen
dc.subjectPhylogeneticsen
dc.subjectKinetic modelen
dc.subjectEnzyme evolutionen
dc.subjectSubstitution rateen
dc.titleCharacterizing selective pressures on the pathway for de novo biosynthesis of pyrimidines in yeasten
dc.typeArticleen
dc.identifier.eissn1471-2148en
dc.contributor.departmentDepartment of Molecular Biology, University of Wyomingen
dc.contributor.departmentDepartment of Biology and Center for Computational Genetics and Genomics, Temple Universityen
dc.contributor.departmentDivision of Epidemiology and Biostatistics, Mel and Enid Zuckerman College of Public Health, University of Arizonaen
dc.contributor.departmentDepartment of Biology and Lund Protein Production Platform, Lund Universityen
dc.contributor.departmentDepartment of Molecular and Cellular Biology, University of Arizonaen
dc.identifier.journalBMC Evolutionary Biologyen
dc.description.collectioninformationThis item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at repository@u.library.arizona.edu.en
dc.eprint.versionFinal published versionen
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