MRE: a web tool to suggest foreign enzymes for the biosynthesis pathway design with competing endogenous reactions in mind

Handle URI:
http://hdl.handle.net/10754/619768
Title:
MRE: a web tool to suggest foreign enzymes for the biosynthesis pathway design with competing endogenous reactions in mind
Authors:
Kuwahara, Hiroyuki; Alazmi, Meshari; Cui, Xuefeng; Gao, Xin ( 0000-0002-7108-3574 )
Abstract:
To rationally design a productive heterologous biosynthesis system, it is essential to consider the suitability of foreign reactions for the specific endogenous metabolic infrastructure of a host. We developed a novel web server, called MRE, which, for a given pair of starting and desired compounds in a given chassis organism, ranks biosynthesis routes from the perspective of the integration of new reactions into the endogenous metabolic system. For each promising heterologous biosynthesis pathway, MRE suggests actual enzymes for foreign metabolic reactions and generates information on competing endogenous reactions for the consumption of metabolites. These unique, chassis-centered features distinguish MRE from existing pathway design tools and allow synthetic biologists to evaluate the design of their biosynthesis systems from a different angle. By using biosynthesis of a range of high-value natural products as a case study, we show that MRE is an effective tool to guide the design and optimization of heterologous biosynthesis pathways. The URL of MRE is http://www.cbrc.kaust.edu.sa/mre/.
KAUST Department:
Computational Bioscience Research Center (CBRC)
Citation:
MRE: a web tool to suggest foreign enzymes for the biosynthesis pathway design with competing endogenous reactions in mind 2016, 44 (W1):W217 Nucleic Acids Research
Publisher:
Oxford University Press (OUP)
Journal:
Nucleic Acids Research
Issue Date:
29-Apr-2016
DOI:
10.1093/nar/gkw342
Type:
Article
ISSN:
0305-1048; 1362-4962
Sponsors:
King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR) [URF/1/1976-04]. Funding for open access charge: King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR) [URF/1/1976-04]. Conflict of interest statement. None declared.
Additional Links:
http://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gkw342
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Articles

Full metadata record

DC FieldValue Language
dc.contributor.authorKuwahara, Hiroyukien
dc.contributor.authorAlazmi, Mesharien
dc.contributor.authorCui, Xuefengen
dc.contributor.authorGao, Xinen
dc.date.accessioned2016-09-04T08:10:49Z-
dc.date.available2016-09-04T08:10:49Z-
dc.date.issued2016-04-29-
dc.identifier.citationMRE: a web tool to suggest foreign enzymes for the biosynthesis pathway design with competing endogenous reactions in mind 2016, 44 (W1):W217 Nucleic Acids Researchen
dc.identifier.issn0305-1048-
dc.identifier.issn1362-4962-
dc.identifier.doi10.1093/nar/gkw342-
dc.identifier.urihttp://hdl.handle.net/10754/619768-
dc.description.abstractTo rationally design a productive heterologous biosynthesis system, it is essential to consider the suitability of foreign reactions for the specific endogenous metabolic infrastructure of a host. We developed a novel web server, called MRE, which, for a given pair of starting and desired compounds in a given chassis organism, ranks biosynthesis routes from the perspective of the integration of new reactions into the endogenous metabolic system. For each promising heterologous biosynthesis pathway, MRE suggests actual enzymes for foreign metabolic reactions and generates information on competing endogenous reactions for the consumption of metabolites. These unique, chassis-centered features distinguish MRE from existing pathway design tools and allow synthetic biologists to evaluate the design of their biosynthesis systems from a different angle. By using biosynthesis of a range of high-value natural products as a case study, we show that MRE is an effective tool to guide the design and optimization of heterologous biosynthesis pathways. The URL of MRE is http://www.cbrc.kaust.edu.sa/mre/.en
dc.description.sponsorshipKing Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR) [URF/1/1976-04]. Funding for open access charge: King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR) [URF/1/1976-04]. Conflict of interest statement. None declared.en
dc.language.isoenen
dc.publisherOxford University Press (OUP)en
dc.relation.urlhttp://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gkw342en
dc.rightsThis is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.comen
dc.titleMRE: a web tool to suggest foreign enzymes for the biosynthesis pathway design with competing endogenous reactions in minden
dc.typeArticleen
dc.contributor.departmentComputational Bioscience Research Center (CBRC)en
dc.identifier.journalNucleic Acids Researchen
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)en
kaust.authorKuwahara, Hiroyukien
kaust.authorAlazmi, Mesharien
kaust.authorCui, Xuefengen
kaust.authorGao, Xinen
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