Molecular tools for chemical biotechnology

Abstract

Biotechnological production of high value chemical products increasingly involves engineering in vivo multi-enzyme pathways and host metabolism. Recent approaches to these engineering objectives have made use of molecular tools to advance de novo pathway identification, tunable enzyme expression, and rapid pathway construction. Molecular tools also enable optimization of single enzymes and entire genomes through diversity generation and screening, whole cell analytics, and synthetic metabolic control networks. In this review, we focus on advanced molecular tools and their applications to engineered pathways in host organisms, highlighting the degree to which each tool is generalizable.

Figure 1

Molecular tools to advance engineering of multi-enzyme biochemical pathways for chemical biotechnology. (a) Genetic and genomic databases are used with predictive algorithms to design pathways, which are then genetically constructed in vitro and/or in vivo. (b) Dynamic control elements allow enzyme expression levels to vary in response to small molecule concentrations. (c) Rounds of diversity generation and screening, informed by machine learning and design of experiment algorithms, generate optimized enzyme variants. (d) Whole cell read-outs provide data for systems level analysis and prediction of specific changes to enable global phenotypic improvements.