Engineering of cell factories for the production of natural products

Driven by massive technological progress in the last decade, natural products research is currently undergoing a transformation: novel high-resolution spectroscopic technologies now allow much better characterization of the molecules present in small amounts, sometimes even in complex mixtures. Combining the progress in analytical technology with cheminformatics approaches, like molecular networking, yields novel opportunities also feasible for high throughput metabolomics applications. Such methods and technologies have been recently reviewed in the Natural Product Reports themed collection on New methods for isolation and structure determination of natural products.¹

This themed issue on Engineering of cell factories for the production of natural products complements that aspect by focusing on the “microbial counterpart” of the recent technology advancement. Recent breakthroughs, such as cheap high-throughput and high-quality sequencing technologies and highly efficient genome editing tools enable approaches that were unthinkable – or at least unfinanceable – only a few years ago.

These technologies simplify and dramatically speed up the identification of biosynthetic gene clusters encoding the biosynthesis of often very complicated molecules.² Modern molecular biology methods, like large gene cluster cloning or genome editing via various CRISPR-based methods, now provide much easier ways to engineer the production of natural products. While many of these tools have just emerged from their “infancy”, they already offer tremendous potential for accessing nature’s diversity of natural products. They open the path to rational engineering of cell factories for the production and optimization of these compounds. Various key aspects and developments are addressed in this Natural Product Reports themed issue:

In a viewpoint article, Jens Nielsen elucidates the state of the art of cell factory engineering and the challenges that our community must address to design and implement the next generation of natural product cell factories (DOI: 10.1039/c9np00005d). One crucial requirement to design such cell factories is the possibility to efficiently manipulate the genomes of the producing microorganisms. As in many fields of modern molecular biology, the application of CRISPR genome editing tools is also starting to transform natural product engineering. Two articles cover this field. Tong et al. introduce the CRISPR technology and review its applications, potential and limitations for various bacterial and fungal producers of natural products (DOI: 10.1039/c8np00089a). Alberti and Corre provide a detailed analysis of CRISPR systems used for engineering streptomycetes, a group of bacteria famous for their potential to synthesize natural products (DOI: 10.1039/c8np00081f). One severe bottleneck in using these and also other genetic engineering technologies is often the availability of efficient transformation protocols. Musiol-Kroll et al. provide an overview of the various tools and methods that are available to engineer “common” and rare actinomycetes (DOI: 10.1039/c9np00029a).

While direct genetic engineering of the producers is one option, an alternative approach is to clone and express the biosynthetic gene clusters. Zhang et al. review state-of-the-art methods that enable the cloning and heterologous expression of biosynthetic gene clusters and their manipulation (DOI: 10.1039/c9np00025a). Myronovskyi and Luzhetskyy describe the latest state of streptomyces cell factory engineering for heterologous production of natural products (DOI: 10.1039/c9np00023b).

Two reviews cover computational aspects. Alanjary et al. describe state-of-the-art computational strategies for re-engineering non-ribosomal peptide synthetases and modular polyketide biosynthesis assembly lines (DOI: 10.1039/c9np00021f). Adamek et al. provide a review on phylogeny-based methods used to analyze, classify and prioritize natural product biosynthetic gene clusters, and guidelines on best practice when carrying out phylogenetic analyses (DOI: 10.1039/c9np00027e).

While a lot of the methods mentioned above were originally developed for studying well-known secondary metabolite/specialized metabolite producing organisms, these methods are now used to expand natural product research to less-studied groups of organisms. In this themed issue, Buijs et al. report on the recent progress that these strategies have allowed in characterizing of marine proteobacteria and their potential to synthesize bioactive natural products (DOI: 10.1039/c9np00020h).

The diverse methods, tools and applications highlighted in this themed issue clearly demonstrate the manifold possibilities that have now begun to open up and the huge future potential of these methods being better integrated. There are exciting times ahead!

References

1. Nat. Prod. Rep., 2019, 36, (6/7), themed collection on New methods for isolation and structure determination of natural products.
2. E. Palazzotto and T. Weber, Curr. Opin. Microbiol., 2018, 45, 109–116.

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