Multi-chassis engineering for heterologous production of microbial natural products

Jing Ke,Yasuo Yoshikuni

doi:10.1016/j.copbio.2019.09.005

Abstract

Microbial genomes encode numerous biosynthetic gene clusters (BGCs) that may produce natural products with diverse applications in medicine, agriculture, the environment, and materials science. With the advent of genome sequencing and bioinformatics, heterologous expression of BGCs is of increasing interest in bioactive natural product (NP) discovery. However, this approach has had limited success because expression of BGCs relies heavily on the physiology of just a few commonly available host chassis. Expanding and diversifying the chassis portfolio for heterologous BGC expression may greatly increase the chances for successful NP production. In this review, we first discuss genetic and genome engineering technologies used to clone, modify, and transform BGCs into multiple strains and to engineer chassis strains. We then highlight studies that employed the multi-chassis approach successfully to optimize NP production, discover previously uncharacterized NPs, and better understand BGC function.

Highlights

Microorganisms provide a variety of bioactive natural products (NPs) used in medicine and agriculture, as well as in protection of the environment and development of materials [1,2,3]
NP biosynthesis pathways are encoded by biosynthetic gene clusters (BGCs), which are often found in a single large, contiguous genomic region
For functional expression of NPs, synthetic biology approaches such as codon optimization, refactoring, and/or DNA synthesis can theoretically be used to uncouple BGCs from their native regulatory constraints [7,8,9,10]. This approach requires carefully adapting the BGC to a species currently available for heterologous expression, such as Escherichia coli, Bacillus subtilis, or Streptomyces lividans

Summary

Introduction

Microorganisms provide a variety of bioactive natural products (NPs) used in medicine and agriculture (e.g. antibiotics and pesticides), as well as in protection of the environment and development of materials [1,2,3]. For functional expression of NPs, synthetic biology approaches such as codon optimization, refactoring, and/or DNA synthesis can theoretically be used to uncouple BGCs from their native regulatory constraints [7,8,9,10] This approach requires carefully adapting the BGC to a species currently available for heterologous expression, such as Escherichia coli, Bacillus subtilis, or Streptomyces lividans. Brophy et al recently developed a transposon mini-ICE from B. subtilis (ICEBs1) [32] This mini-ICEBs1 element achieved efficient transfer of large DNA constructs (100 kb) into 35 firmicute strains isolated from humans and soil. While these attP-int systems are powerful tools to domesticate previously undomesticated strains, their host ranges are usually limited to a small group of bacteria. A landing pad (LP) containing mutually exclusive lox sites is first www.sciencedirect.com

17 Metatricycloene

13. Bibb MJ

34. Baltz RH

Findings

42. Chin JW