TY - JOUR
T1 - MRE: a web tool to suggest foreign enzymes for the biosynthesis pathway design with competing endogenous reactions in mind
AU - Kuwahara, Hiroyuki
AU - Alazmi, Meshari
AU - Cui, Xuefeng
AU - Gao, Xin
N1 - KAUST Repository Item: Exported on 2020-10-01
Acknowledged KAUST grant number(s): URF/1/1976-04
Acknowledgements: 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.
PY - 2016/4/29
Y1 - 2016/4/29
N2 - 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/.
AB - 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/.
UR - http://hdl.handle.net/10754/619768
UR - http://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gkw342
UR - http://www.scopus.com/inward/record.url?scp=85018511356&partnerID=8YFLogxK
U2 - 10.1093/nar/gkw342
DO - 10.1093/nar/gkw342
M3 - Article
C2 - 27131375
SN - 0305-1048
VL - 44
SP - W217-W225
JO - Nucleic Acids Research
JF - Nucleic Acids Research
IS - W1
ER -