title: MRE: a web tool to suggest foreign enzymes for the biosynthesis pathway design with competing endogenous reactions in mind.
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/.
authors.affiliation: King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, 23955, Saudi Arabia.
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Kuwahara
authors.affiliation: King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, 23955, Saudi Arabia.
authors.forename: Meshari
authors.initials: M
authors.lastname: Alazmi
authors.affiliation: King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, 23955, Saudi Arabia.
authors.forename: Xuefeng
authors.initials: X
authors.lastname: Cui
authors.affiliation: King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, 23955, Saudi Arabia xin.gao@kaust.edu.sa.
authors.forename: Xin
authors.initials: X
authors.lastname: Gao
mesh_terms: D037621:Artemisinins / Q000378:metabolism; D003196:Computer Graphics; D004926:Escherichia coli / Q000201:enzymology / Q000235:genetics*; D044950:Flavanones / Q000096:biosynthesis; D015870:Gene Expression; D005990:Glycerol / Q000378:metabolism; D020407:Internet; D007700:Kinetics; D060847:Metabolic Engineering; D053858:Metabolic Networks and Pathways / Q000235:genetics*; D012441:Saccharomyces cerevisiae / Q000201:enzymology / Q000235:genetics*; D012984:Software; D013045:Species Specificity; D058615:Synthetic Biology / Q000379:methods*; D013816:Thermodynamics; D019076:Transgenes
chemical_list: D037621:Artemisinins; D044950:Flavanones; C047721:artemisic acid; C005273:naringenin; D005990:Glycerol