Yeast metabolic chassis designs for diverse biotechnological products

Abstract

The diversity of industrially important molecules for which microbial production routes have been experimentally demonstrated is rapidly increasing. The development of economically viable producer cells is, however, lagging behind, as it requires substantial engineering of the host metabolism. A chassis strain suitable for production of a range of molecules is therefore highly sought after but remains elusive. Here, we propose a genome-scale metabolic modeling approach to design chassis strains of Saccharomyces cerevisiae – a widely used microbial cell factory. For a group of 29 products covering a broad range of biochemistry and applications, we identified modular metabolic engineering strategies for re-routing carbon flux towards the desired product. We find distinct product families with shared targets forming the basis for the corresponding chassis cells. The design strategies include overexpression targets that group products by similarity in precursor and cofactor requirements, as well as gene deletion strategies for growth-product coupling that lead to non-intuitive product groups. Our results reveal the extent and the nature of flux re-routing necessary for producing a diverse range of products in a widely used cell factory and provide blueprints for constructing pre-optimized chassis strains.

Genome scale metabolic modeling reveals the metabolic potential of three Type II methanotrophs of the genus Methylocystis

“…A large variety of industrially relevant products can be synthesized by M. hirsuta from a small number of metabolic precursors (Jouhten et. al., 2016), some key precursors and final products are summarized in Table 3.…”

Mitochondrial respiration is required to provide amino acids during fermentative proliferation of fission yeast

“…These catabolic processes yield energy in the form of ATP, reducing equivalents in the form of NAD(P)H and FADH, as well as a series of intermediates required for anabolic (biosynthetic) metabolism. The flux distributions between all three pathways are dynamically adjusted by the cell to achieve an optimal level of growth and resilience given a specific lifestyle, stress condition or ecological niche (Ralser et al , 2007; Peralta et al , 2015; Jouhten et al , 2016; Nidelet et al , 2016; Olin‐Sandoval et al , 2019). These metabolic adaptations are of fundamental importance for cellular physiology as they determine their tolerance for changing conditions and stress (Lahtvee et al , 2016).…”

Rapid pathway prototyping and engineering using in vitro and in vivo synthetic genome SCRaMbLE-in methods

“…Besides the expression level of the target genes, the choice of host and the genetic background of the host is of vital importance for heterologous pathway production 27 , 28 . Repressing competing pathways and knocking out non-essential genes interacting with the target pathway can re-direct the precursor transformation fluxes in the metabolic maps or remove toxicity of side products to potentially achieve higher target production.…”