Synthetic biology design tools for metabolic engineering

Pablo Carbonell

ai2, Polytechnic University of Valencia (Universitat Politècnica de València), Valencia, Spain.

Abstract

Metabolic engineering (i.e., optimizing genetic and regulatory genes in cell factories) is challenged nowadays by the social expectation of a technology that can deliver a breadth of distinctive biomolecules to cope with the increasing demand of key bio-based chemicals as alternatives to oil-based chemistry in the newly bio-economy of green reconstruction. In such new bio-economy, times from concept to development and to scale-up of biomolecules become major industrial assets. Automated workflows that exploit the capabilities of synthetic biology design tools are thus required to underpin successful metabolic engineering protocols going from concept to biomanufacturing production pipelines. In this chapter, we survey leading synthetic biology design tools for metabolic engineering and explore the strategies for delivering high-performance microbial cell factories of biomolecules. Current tools for modeling, pathway and experimental design, pathway dynamic regulation, and machine learning are described, and their enabling role as key tools in the metabolic engineering biomanufacturing workflow will be assessed and highlighted.

Keywords: Metabolic engineering, Synthetic biology, Metabolic pathway design, Experimental design, Dynamic regulation, Machine learning, Automation.