Bacteria have historically been a rich source of natural products ( e.g. polyketides and non-ribosomal peptides) that possess medically-relevant activities. Despite extensive discovery programs in both industry and academia, a plethora of biosynthetic pathways remain uncharacterized and the corresponding molecular products untested for potential bioactivities. This knowledge gap comes in part from the fact that many putative natural product producers have not been cultured in conventional laboratory settings in which the corresponding products are produced at detectable levels. Next-generation sequencing technologies are further increasing the knowledge gap by obtaining metagenomic sequence information from complex communities where production of the desired compound cannot be isolated in the laboratory. For these reasons, many groups are turning to synthetic biology to produce putative natural products in heterologous hosts. This strategy depends on the ability to heterologously express putative biosynthetic gene clusters and produce relevant quantities of the corresponding products. Actinobacteria remain the most abundant source of natural products and the most promising heterologous hosts for natural product discovery and production. However, researchers are discovering more natural products from other groups of bacteria, such as myxobacteria and cyanobacteria. Therefore, phylogenetically similar heterologous hosts have become promising candidates for synthesizing these novel molecules. The downside of working with these microbes is the lack of well-characterized genetic tools for optimizing expression of gene clusters and product titers. This review examines heterologous expression of natural product gene clusters in terms of the motivations for this research, the traits desired in an ideal host, tools available to the field, and a survey of recent progress.
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Bacterial natural product discovery by heterologous expression
Natural products have found important applications in the pharmaceutical and agricultural sectors. In bacteria, the genes that encode the biosynthesis of natural products are often colocalized in the genome, forming biosynthetic gene clusters. It has been predicted that only 3% of natural products encoded in bacterial genomes have been discovered thus far, in part because gene clusters may be poorly expressed under laboratory conditions. Heterologous expression can help convert bioinformatics predictions into products. However, challenges remain, such as gene cluster prioritization, cloning of the complete gene cluster, high level expression, product identification, and isolation of products in practical yields. Here we reviewed the literature from the past 5 years (January 2018 to June 2023) to identify studies that discovered natural products by heterologous expression. From the 50 studies identified, we present analyses of the rationale for gene cluster prioritization, cloning methods, biosynthetic class, source taxa, and host choice. Combined, the 50 studies led to the discovery of 63 new families of natural products, supporting heterologous expression as a promising way to access novel chemistry. However, the success rate of natural product detection varied from 11% to 32% based on four large-scale studies that were part of the reviewed literature. The low success rate makes it apparent that much remains to be improved. The potential reasons for failure and points to be considered to improve the chances of success are discussed.
At least 63 new families of bacterial natural products were discovered using heterologous expression in the last 5 years, supporting heterologous expression as a promising way to access novel chemistry; however, the success rate is low (11–32%) making it apparent that much remains to be improved—we discuss the potential reasons for failure and points to be considered to improve the chances of success. BioRender was used to generate the graphical abstract figure.
- Award ID(s):
- 2237551
- NSF-PAR ID:
- 10480445
- Publisher / Repository:
- Oxford University Press
- Date Published:
- Journal Name:
- Journal of Industrial Microbiology and Biotechnology
- Volume:
- 50
- Issue:
- 1
- ISSN:
- 1367-5435
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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