Bioprospecting Through Cloning of Whole Natural Product Biosynthetic Gene Clusters.

Zhenquan Lin,Zihe Liu,Jens Nielsen

doi:10.3389/fbioe.2020.00526

Abstract

Since the discovery of penicillin, natural products and their derivatives have been a valuable resource for drug discovery. With recent development of genome mining approaches in the post-genome era, a great number of natural product biosynthetic gene clusters (BGCs) have been identified and these can potentially be exploited for the discovery of novel natural products that can find application as pharmaceuticals. Since many BGCs are silent or do not express in native hosts under laboratory conditions, heterologous expression of BGCs in genetically tractable hosts becomes an attractive route to activate these BGCs to discover the corresponding products. Here, we highlight recent achievements in cloning and discovery of natural product biosynthetic pathways via intact BGC capturing, and discuss the prospects of high-throughput and multiplexed cloning of rational-designed gene clusters in the future.

Highlights

Natural products produced by plant, bacteria, and fungi have served as a crucial source of pharmaceuticals, therapeutic agents and industrially useful compounds, such as antibiotic, antitumor, and anti-infective drugs (Nielsen, 2019)
The development of advancing genome editing tools, such as clustered regularly interspaced short palindromic repeat–CRISPR-associated protein (CRISPR-Cas) system, has substantially accelerated the process of direct cloning and made it possible to isolate the exact sequence of target biosynthetic gene clusters (BGCs) in vitro (Lee et al, 2015; Wang et al, 2018; Tao et al, 2019)
With current technologies it is still challenging to combine the advantages of both methods, and to use direct cloning methods to test all predictive BGCs from an entire genome in a single reaction

Summary

Introduction

Natural products produced by plant, bacteria, and fungi have served as a crucial source of pharmaceuticals, therapeutic agents and industrially useful compounds, such as antibiotic, antitumor, and anti-infective drugs (Nielsen, 2019). With the development of sequencing technologies, the costs of genome sequencing has been reduced, and hereby metagenomics has emerged as a strategic approach to explore unculturable microbes through the sequencing and analysis of environmental DNA. Hereby massive DNA sequence information has become accessible. Many bioinformatic tools have been developed to uncover putative BGCs, such as antiSMASH 5.0 (Blin et al, 2019), BiG-SCAPE (Navarro-Muñoz et al, 2019), PRISM 3 (Skinnider et al, 2017), MIBiG 2.0 (Kautsar et al, 2019), RODEO (Tietz et al, 2017), and genomescale metabolic models (Nielsen and Nielsen, 2017). There are many technical challenges to translate these putative BGCs into specialized chemicals, resulting in a huge gap in the natural product discover pipeline (Dejong et al, 2016)

Methods

Findings

Conclusion