Rational Metabolic Pathway Prediction and Design: Computational Tools and Their Applications for Yeast Systems and Synthetic Biology

Abstract

Continuous progress in metabolic engineering of microbial cell factories like yeast requires the support of computational tools for finding novel unintuitive biotransformations routes. In this chapter, a succinct overview is provided of the most relevant computational tools for pathway prediction by retro-biosynthesis, and pathway design through stoichiometry-based optimization methods. Illustrative case studies are also presented showcasing different strategies for pathway optimization in yeast, namely redox cofactor balancing, improved precursor supply, and heterologous expression of carbon fixation pathways. Finally, challenges and limitations hindering the broad adoption and implementation of these tools for metabolic engineering will be discussed.