Accessing Nature’s diversity through metabolic engineering and synthetic biology

Abstract

In this perspective, we highlight recent examples and trends in metabolic engineering and synthetic biology that demonstrate the synthetic potential of enzyme and pathway engineering for natural product discovery. In doing so, we introduce natural paradigms of secondary metabolism whereby simple carbon substrates are combined into complex molecules through “scaffold diversification”, and subsequent “derivatization” of these scaffolds is used to synthesize distinct complex natural products. We provide examples in which modern pathway engineering efforts including combinatorial biosynthesis and biological retrosynthesis can be coupled to directed enzyme evolution and rational enzyme engineering to allow access to the “privileged” chemical space of natural products in industry-proven microbes. Finally, we forecast the potential to produce natural product-like discovery platforms in biological systems that are amenable to single-step discovery, validation, and synthesis for streamlined discovery and production of biologically active agents.

Using natural products for drug discovery: the impact of the genomics era

“…The explosion of BGC sequence information offers critical insights into how remarkably complex natural products covering vast biologically relevant chemical structure space are assembled from a limited set of simple building blocks [115]. BGCs generally encode two groups of biosynthetic enzymes – one group generates key biosynthetic precursors and assembles the core scaffold while the other group derivatizes the scaffolds [116].…”

“…alkylation, acylation, oxidation, glycosylation) of natural product scaffolds allows exploration of a defined chemical structure-function space. Naturally occurring and engineered P450s and glycosyltransferases exhibiting broad substrate specificities have been successfully employed for late-stage derivatization of terpenes, PKs and NRPs [115]. New sulfated glycopeptide congeners were obtained in vitro and in vivo by exploiting eDNA-derived sulfotransferases frequently associated with glycopeptide BGCs [120].…”

Twenty‐first‐century chemical odyssey: fuels versus commodities and cell factories versus chemical plants

“…A key focus of a number of research programmes is the design of genetic constructs containing the information necessary to synthesize the product(s) of interest from specific substrate(s). Despite this effervescence in the knowledge of molecular microbial ecology and bioinformatics (King et al, 2016), the number of biochemicals (referred to here as a chemical produced by a living organism) made in recent years at pilot-industrial scale is very modest. A question arisescan biochemicals made from renewable sources replace chemicals (here the term is used to refer to molecules made in the chemical realm), particularly when large amounts are required such as in the world of commodities?…”

Emerging tools, enabling technologies, and future opportunities for the bioproduction of aromatic chemicals

“…In recent years, significant and growing interest has emerged in the development of alternative, microbial production routes for aromatic chemicals from renewable, biomass‐derived substrates. Such efforts have been aided by advancements in metabolic engineering, protein engineering, and systems and synthetic biology, which continue to guide both rational and combinatorial approaches towards efficient biocatalyst development. As a result, the de novo biosynthesis of a diversity of different aromatic chemicals is now a reality, with applications that, like their petroleum‐derived counterparts, include bulk chemicals and plastics, specialty chemicals, flavors and fragrances, and pharmaceuticals and nutraceuticals (Fig.…”