New tools for reconstruction and heterologous expression of natural product biosynthetic gene clusters

Abstract

Natural product scaffolds remain a major source and inspiration for human therapeutics. However, generation of a natural product in the post-genomic era often requires reconstruction of the corresponding biosynthetic gene cluster in a heterologous host. In the burgeoning fields of synthetic biology and metabolic engineering, a significant amount of efforts has been devoted to develop DNA assembly techniques with higher efficiency, fidelity, and modularity, and heterologous expression systems with higher productivity and yield. Here we describe recent advances in DNA assembly and host engineering and highlight their applications in natural product discovery and engineering.

De novo Biosynthesis of “Non‐Natural” Thaxtomin Phytotoxins

“…However there are many microorganisms that produce useful secondary metabolites, which are not amenable to such genetic manipulation. The rise of synthetic biology has provided access to larger synthetic DNA constructs, rapid DNA capture,7, 8, 9 editing,10, 11 assembly,12, 13 and other advances 14, 15. The prospect of using these new tools to assemble de novo biosynthetic pathways in well‐characterized heterologous host strains16, 17 for diversification and optimization of natural products, derived from less tractable microorganisms, is an attractive goal.…”

Antibiotic discovery is a walk in the park

“…Although still not trivial, the improvement in the past decade in methods for assembling long genetic constructs in a different species host (17), yield optimization by pathway manipulation (18), and combinatorial biosynthesis (19) offer an exciting toolbox for accessing this molecular biodiversity.…”

Omics-based natural product discovery and the lexicon of genome mining

“…Both of these experimental approaches have unique challenges that vary with the organism being studied. Nonetheless, progress has been made in the automation of heterologous expression systems[16] and in retro-biosynthetic approaches to link orphan BGCs to known compounds[17] thus suggesting that this bottleneck may ultimately be overcome through advances in synthetic and computational biology. Meanwhile, the relatively few BGCs that have been experimentally characterized (1,393 BGCs in MIBiG as of May 2017) relative to the considerably larger number of microbial NPs discovered over the last 50-plus years (52,395 microbial NPs[18]) raises the generally understated possibility that much of the apparent genetic potential observed in bacterial genome sequences has already been realized.…”