Challenges and Advances in Genome Editing Technologies in Streptomyces

Abstract

The genome of Streptomyces encodes a high number of natural product (NP) biosynthetic gene clusters (BGCs). Most of these BGCs are not expressed or are poorly expressed (commonly called silent BGCs) under traditional laboratory experimental conditions. These NP BGCs represent an unexplored rich reservoir of natural compounds, which can be used to discover novel chemical compounds. To activate silent BGCs for NP discovery, two main strategies, including the induction of BGCs expression in native hosts and heterologous expression of BGCs in surrogate Streptomyces hosts, have been adopted, which normally requires genetic manipulation. So far, various genome editing technologies have been developed, which has markedly facilitated the activation of BGCs and NP overproduction in their native hosts, as well as in heterologous Streptomyces hosts. In this review, we summarize the challenges and recent advances in genome editing tools for Streptomyces genetic manipulation with a focus on editing tools based on clustered regularly interspaced short palindrome repeat (CRISPR)/CRISPR-associated protein (Cas) systems. Additionally, we discuss the future research focus, especially the development of endogenous CRISPR/Cas-based genome editing technologies in Streptomyces.

In vitro Cas9-assisted editing of modular polyketide synthase genes to produce desired natural product derivatives

“…In the conventional method, the derivatives of the target compounds were produced by the wild-type producer. Many strategies for genome editing of Streptomyces using CRISPR/Cas9 technology in vivo have been developed 37,38 ; however, it is still challenging to introduce a large DNA fragment into non-model host strains and to avoid off-targets especially in the PKS genes. In contrast, our approach is based on the high probability of heterologous expression in a versatile host.…”

Antimicrobial Stewardship: Fighting Antimicrobial Resistance and Protecting Global Public Health

“…Significant developments in genetic engineering techniques can effectively help target and alter pathogenic bacterial genomes to recognize and mitigate drug resistance mechanisms. 188 , 189 The clustered regularly interspaced short palindromic repeats – CRISPR-associated (CRISPR-Cas) system, a bacterial adaptive immune system, is a newly recognized approach for controlling antibiotic-resistant strains, utilizing genomic engineering tools geared for gene knock-out and knock-in of sequence-specific DNA antibiotic targets. 189–191 The system is aimed to neutralize “the invasion by foreign genetic material” such as, bacteriophages, plasmids and transposons where the CRISPR-Cas9 acts as a “RNA-guided-DNA cutter”.…”

Faculty Opinions recommendation of In vitro Cas9-assisted editing of modular polyketide synthase genes to produce desired natural product derivatives.

“…Many strategies for genome editing of Streptomyces using CRISPR/Cas9 technology in vivo have been developed 37,38 ; however, it is still challenging to introduce a large DNA fragment into non-model host strains and to avoid off-targets especially in the PKS genes. In contrast, our approach is based on the high probability of heterologous expression in a versatile host.…”