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Synthetic biology to access and expand nature's chemical diversity

Key Points

  • This Review covers the recent advances in synthetic biology and how these advances will affect the field of natural products.

  • There has been an emphasis on creating genetic parts, such as promoters, that generate precise levels of gene expression. The generation of large libraries of well-characterized parts and the development of biophysical and bioinformatic models to predict the behaviour of genetic parts in different organisms will aid in the transfer of biosynthetic gene clusters between hosts.

  • The capacity of DNA synthesis has exploded over the past decade and it is routine to synthesize the 20–100 kb required for a large gene cluster. In addition, new DNA assembly methods enable the rapid construction of different genetic part permutations or to substitute many genetic parts in a single step.

  • With regard to synthetic regulation, genetic circuits have been constructed that function as logic gates, timers, switches and oscillators. Sensors have also been developed that respond to many inducible inputs as well as metabolite levels. These could be incorporated into natural product pathways to control the timing of expression of different genes or to implement feedback in response to a toxic intermediate.

  • It is often desirable to make many simultaneous genomic changes. Methods such as CRISPR–Cas9 can target essentially any region of the genome and have been shown to function in many species, including several host species that are well suited for the industrial-scale production of small molecules.

Abstract

Bacterial genomes encode the biosynthetic potential to produce hundreds of thousands of complex molecules with diverse applications, from medicine to agriculture and materials. Accessing these natural products promises to reinvigorate drug discovery pipelines and provide novel routes to synthesize complex chemicals. The pathways leading to the production of these molecules often comprise dozens of genes spanning large areas of the genome and are controlled by complex regulatory networks with some of the most interesting molecules being produced by non-model organisms. In this Review, we discuss how advances in synthetic biology — including novel DNA construction technologies, the use of genetic parts for the precise control of expression and for synthetic regulatory circuits — and multiplexed genome engineering can be used to optimize the design and synthesis of pathways that produce natural products.

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Figure 1: Natural product biosynthetic gene clusters.
Figure 2: Genetic refactoring and genetic parts for controlling levels of gene expression.
Figure 3: Advanced regulation relevant to natural product biosynthesis.
Figure 4: Using refactored systems for genetic optimization and host transfer.
Figure 5: Multiplexed genome editing with CRISPR–Cas9.

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Glossary

Polyketide

One of a family of natural products that share a common biosynthetic pathway through the decarboxylative condensation of substituted malonyl-CoA-derived extender units and acyl-CoA starter units on polyketide synthase enzymes.

Non-ribosomal peptide

One of a family of natural products that share a common biosynthetic pathway through the condensation of proteogenic or non-proteogenic amino acids on modular non-ribosomal peptide synthetase enzymes.

Terpene

One of a family of natural products that share a common biosynthetic pathway through the polymerization of branched five-carbon isoprene units and cyclization by terpene synthases.

Ribosomally synthesized and post-translationally modified peptide

(RiPP). One of a family of natural products, including the lanthipeptides, bacteriocins, and thiazole-modified or oxazole-modified microcins, that share a common biosynthetic pathway through the translation of an mRNA-encoded core peptide and subsequent modification.

Random chemical mutagenesis

A process by which cells or organisms are exposed to chemical mutagens to introduce mutations at random locations in the genome.

5′ untranslated region

(5′ UTR). The untranslated region of an mRNA transcript that is upstream of the start codon. The sequence of the 5′ UTR can influence translation initiation and mRNA stability.

Bicistrons

Transcripts that contain two coding DNA sequences (CDSs). For translational control, the first CDS encodes a short, non-functional peptide and is located immediately upstream of the ribosome binding site for the second CDS.

Actinorhodin

A benzoisochromanequinone polyketide pigment produced by Streptomyces coelicolor.

para-aminostyrene

An industrially relevant vinyl aromatic monomer with applications in materials and biomedicine.

Undecylprodigiosin

A tripyrrole polyketide pigment produced by Streptomyces coelicolor.

Gibson assembly

A restriction-enzyme-independent method for the joining of several DNA fragments in a single isothermal reaction.

Pristinamycin II

One of two structurally unrelated chemical components of the clinical antibiotic pristinamycin. Pristinamycin II is a depsipeptide antibiotic produced by Streptomyces pristinaespiralis.

Catechin

A plant flavonoid with antioxidant properties.

Indolocarbazoles

A family of five-ring heterocyclic aromatic compounds that share a common biosynthetic pathway from two tryptophan molecules.

Platencin

An antibiotic produced by Streptomyces platensis containing an amino-dihydroxybenzoic acid moiety fused to a modified diterpene core.

Shunt metabolites

Chemically modified intermediates of a biosynthetic pathway that can no longer proceed through the biosynthetic pathway.

Tylosin

A glycosylated macrolide antibiotic produced by Streptomyces venezuelae.

Okazaki fragments

Short, newly synthesized single-stranded DNA oligomers that are formed on the lagging template strand during DNA replication.

Lycopene

A symmetrical tetraterpene pigment formed by the tail-to-tail condensation of two molecules of geranylgeranyl diphosphate.

T7 RNA polymerase promoters

Short DNA sequences that are recognized by T7 RNA polymerase to initiate transcription.

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Smanski, M., Zhou, H., Claesen, J. et al. Synthetic biology to access and expand nature's chemical diversity. Nat Rev Microbiol 14, 135–149 (2016). https://doi.org/10.1038/nrmicro.2015.24

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