From random mutagenesis to systems biology in metabolic engineering of mammalian cells

Abstract

Metabolic engineering is rapidly developing, with a continuous stream of technological developments being employed to expand the portfolio of molecules produced in cell factories. For chemical production (e.g., amino acids, biofuels, among others), metabolic engineering has progressed through three phases [1]. Initially, biological products were obtained through random mutagenesis of production strains and large screening efforts. Improved microbial strains could be isolated, but mechanisms underlying the desired phenotype were often poorly understood [2]. Diverse molecular biology techniques facilitated the second phase, in which simple, intuitive modifications were made. The third phase now employs systems biology techniques to understand the effect of modifications on all other metabolic pathways and on cell physiology. Thus, we have entered an era in which metabolic engineering aims to improve microbial strains in a reproducible fashion, using complex designs based on detailed biochemical knowledge and computational model simulations. Here, we highlight the historical progression toward using systems biology in microbial metabolic engineering and compare this to the current status of mammalian production cell line development. Finally, we discuss the unique challenges in engineering mammalian cell lines for biotherapeutic production and outline how systems biology can facilitate metabolic engineering efforts for these platforms. The systems biology approach to metabolic engineering has been enabled by three primary advancements: whole-genome sequencing, gene editing tools and genome-scale models of cellular metabolism. The completion of the Escherichia coli K-12 genome sequencing effort in 1997 [3] provided a comprehensive parts list for targeted metabolic engineering and expanded the scope of our understanding of the machinery within this microbe. The further development of efficient genetic modification systems, such as the lambda Red recombination system [4], enabled the deployment of targeted metabolic engineering designs, such as the removal of competing pathways that divert flux away from the formation of a desired product. Predictions of the systemic effects of genetic modifications were enabled when the information in the sequenced genome was harnessed for the development of genome-scale models of metabolism [5]. These models contain all known biochemical reactions in a cell, thus allowing one to predict the overall impact of modifications on phenotypic traits such as growth rate and small molecule secretion. Systems biology approaches are now important tools in microbial metabolic engineering. Yim et al. genetically modified E. coli to produce 1,4-butanediol (BDO) by introducing heterologous genes to allow Hooman Hefzi Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA