XTMS: pathway design in an eXTended metabolic space.

Pablo Carbonell,Jean-Loup Faulon,Pierre Parutto,Shashi Bhushan Pandit,Joan Herisson

doi:10.1093/nar/gku362

Abstract

As metabolic engineering and synthetic biology progress toward reaching the goal of a more sustainable use of biological resources, the need of increasing the number of value-added chemicals that can be produced in industrial organisms becomes more imperative. Exploring, however, the vast possibility of pathways amenable to engineering through heterologous genes expression in a chassis organism is complex and unattainable manually. Here, we present XTMS, a web-based pathway analysis platform available at http://xtms.issb.genopole.fr, which provides full access to the set of pathways that can be imported into a chassis organism such as Escherichia coli through the application of an Extended Metabolic Space modeling framework. The XTMS approach consists on determining the set of biochemical transformations that can potentially be processed in vivo as modeled by molecular signatures, a specific coding system for derivation of reaction rules for metabolic reactions and enumeration of all the corresponding substrates and products. Most promising routes are described in terms of metabolite exchange, maximum allowable pathway yield, toxicity and enzyme efficiency. By answering such critical design points, XTMS not only paves the road toward the rationalization of metabolic engineering, but also opens new processing possibilities for non-natural metabolites and novel enzymatic transformations.

Highlights

Synthesis of value-added molecules in chassis organisms, such as Escherichia coli and Saccharomyces cerevisiae, through heterologous pathways requires of a careful selection and optimization of each step of the biosynthesis pathway [1, 2]
The gene score is given by the average of each individual score; (iii) Number of steps: Number of enzymatic steps in the pathway; (iv) Number of putative steps: Number of enzymatic steps in the pathway that correspond to putative reactions predicted in the Extended Metabolic Space; (v) Estimated toxicity: Average toxicity log(IC50) for intermediate metabolites in the pathway, evaluated by using the EcoliTox server [32]; (vi) Maximum allowed yield: This value estimates the maximum available yield in the pathway based on estimated fluxes of the precursors of the pathway in a wild-type strain of E. coli obtained by flux balance analysis optimized for growth
A better understanding of the metabolic space and the scope of metabolites that can be synthesized and transformed by enzymes is critical for future development in metabolic engineering and synthetic biology

Summary

Introduction

Synthesis of value-added molecules in chassis organisms, such as Escherichia coli and Saccharomyces cerevisiae, through heterologous pathways requires of a careful selection and optimization of each step of the biosynthesis pathway [1, 2]. We introduce the XTMS web server, an online tool which provides access to the set of available pathways that can be imported into E. coli based on an Extended Metabolic Space, i.e. on the set of potential in vivo biochemical transformations as modeled by molecular signatures [24].

Results

Conclusion