Cell-Free Synthesis of Natural Compounds from Genomic DNA of Biosynthetic Gene Clusters

Cell-free synthetic biology for natural product biosynthesis and discovery

Natural products have applications as biopharmaceuticals, agrochemicals, and other high-value chemicals. However, there are challenges in isolating natural products from their native producers (e.g. bacteria, fungi, plants). In many cases, synthetic chemistry or heterologous expression must be used to access these important molecules. The biosynthetic machinery to generate these compounds is found within biosynthetic gene clusters, primarily consisting of the enzymes that biosynthesise a range of natural product classes (including, but not limited to ribosomal and nonribosomal peptides, polyketides, and terpenoids). Cell-free synthetic biology has emerged in recent years as a bottom-up technology applied towards both prototyping pathways and producing molecules. Recently, it has been applied to natural products, both to characterise biosynthetic pathways and produce new metabolites. This review discusses the core biochemistry of cell-free synthetic biology applied to metabolite production and critiques its advantages and disadvantages compared to whole cell and/or chemical production routes. Specifically, we review the advances in cell-free biosynthesis of ribosomal peptides, analyse the rapid prototyping of natural product biosynthetic enzymes and pathways, highlight advances in novel antimicrobial discovery, and discuss the rising use of cell-free technologies in industrial biotechnology and synthetic biology.

The bacterial symbionts of Entomopathogenic nematodes and their role in symbiosis and pathogenesis

Entomopathogenic bacteria in the genera Xenorhabdus and Photorhabdus are mutualistically associated with entomopathogenic nematodes (EPN) Steinernema and Heterorhabditis, respectively. Together they form an insecticidal partnership which has been shown to kill a wide range of insect species. The spectrum of dependence in this symbiotic partnership is diverse, ranging from a tight, obligate relationship to a facultative one. A body of evidence suggests that the reproductive fitness of the nematode-bacterium partnership is tightly associated and interdependent. Furthermore, maintenance of their virulence is also critical to the conversion of the insect host as a suitable environment where this partnership can be perpetuated. Disruption of the symbiotic partnership can have detrimental effects on the fitness of both partners. The nematode-bacterial symbiont-insect partnership represents a model system in ecology and evolutionary biology and amenable to investigate beneficial and antagonistic interactions between invertebrates and microbes. Furthermore, the EPN's bacterial symbionts are also viewed as a model system to study the biosynthesis, structure and function of various natural products. Their ability to produce up to 25 different natural product classes is outstanding among the Morganellaceae. These natural products show biological activity, most likely originating from important functions during the life cycle of both the nematodes and their symbionts. Tools and high throughput technologies have been developed to identify ubiquitous and rare molecules and study their function and assess their potential as novel biological activities. We herein summarize the symbiotic relationship between EPN and their bacterial symbionts, focusing on their fitness and their ability to successfully access and utilize an insect host. We also recapitulate the history of natural products research highlighting recent findings and the synthetic biology approaches that are currently implemented to identify non-natural derivatives from Xenorhabdus and Photorhabdus with improved biological activity.

Microbial secondary metabolites: advancements to accelerate discovery towards application

Microbial secondary metabolites not only have key roles in microbial processes and relationships but are also valued in various sectors of today's economy, especially in human health and agriculture. The advent of genome sequencing has revealed a previously untapped reservoir of biosynthetic capacity for secondary metabolites indicating that there are new biochemistries, roles and applications of these molecules to be discovered. New predictive tools for biosynthetic gene clusters (BGCs) and their associated pathways have provided insights into this new diversity. Advanced molecular and synthetic biology tools and workflows including cell-based and cell-free expression facilitate the study of previously uncharacterized BGCs, accelerating the discovery of new metabolites and broadening our understanding of biosynthetic enzymology and the regulation of BGCs. These are complemented by new developments in metabolite detection and identification technologies, all of which are important for unlocking new chemistries that are encoded by BGCs. This renaissance of secondary metabolite research and development is catalysing toolbox development to power the bioeconomy.

Application of a Cell-Free Synthetic Biology Platform for the Reconstitution of Teleocidin B and UK-2A Precursor Biosynthetic Pathways

We report the successful cell-free reconstitution of two natural product biosynthetic pathways of divergent complexity and structural classes. We first constructed the teleocidin biosynthetic pathway using our BY-2 (tobacco) cell-free protein synthesis (CFPS) system. We discovered a direct interaction between TleA and MbtH, and showed that the BY-2 system is capable of producing more than 80 mg/L teleocidin B-3 with cofactor supplementation and ∼20 mg/L with no cofactors supplemented, demonstrating the high metabolic activity of the system. We then extended our methodology and report the first successful cell-free biosynthesis of UK-2 diol (precursor to the commercially valuable secondary metabolite UK-2A) from simple building blocks by refactoring a complex pathway of 10 proteins in the wheat germ CFPS system. We show that plant CFPS systems are suitable for reconstructing pathways and identifying the functions of uncharacterized genes linked to biosynthetic gene clusters and rate-limiting biosynthetic steps.

Pigments from pathogenic bacteria: a comprehensive update on recent advances

Bacterial pigments stand out as exceptional natural bioactive compounds with versatile functionalities. The pigments represent molecules from distinct chemical categories including terpenes, terpenoids, carotenoids, pyridine, pyrrole, indole, and phenazines, which are synthesized by diverse groups of bacteria. Their spectrum of physiological activities encompasses bioactive potentials that often confer fitness advantages to facilitate the survival of bacteria amid challenging environmental conditions. A large proportion of such pigments are produced by bacterial pathogens mostly as secondary metabolites. Their multifaceted properties augment potential applications in biomedical, food, pharmaceutical, textile, paint industries, bioremediation, and in biosensor development. Apart from possessing a less detrimental impact on health with environmentally beneficial attributes, tractable and scalable production strategies render bacterial pigments a sustainable option for novel biotechnological exploration for untapped discoveries. The review offers a comprehensive account of physiological role of pigments from bacterial pathogens, production strategies, and potential applications in various biomedical and biotechnological fields. Alongside, the prospect of combining bacterial pigment research with cutting-edge approaches like nanotechnology has been discussed to highlight future endeavours.

Cell-free biosynthesis and engineering of ribosomally synthesized lanthipeptides

Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a major class of natural products with diverse chemical structures and potent biological activities. A vast majority of RiPP gene clusters remain unexplored in microbial genomes, which is partially due to the lack of rapid and efficient heterologous expression systems for RiPP characterization and biosynthesis. Here, we report a unified biocatalysis (UniBioCat) system based on cell-free gene expression for rapid biosynthesis and engineering of RiPPs. We demonstrate UniBioCat by reconstituting a full biosynthetic pathway for de novo biosynthesis of salivaricin B, a lanthipeptide RiPP. Next, we delete several protease/peptidase genes from the source strain to enhance the performance of UniBioCat, which then can synthesize and screen salivaricin B variants with enhanced antimicrobial activity. Finally, we show that UniBioCat is generalizable by synthesizing and evaluating the bioactivity of ten uncharacterized lanthipeptides. We expect UniBioCat to accelerate the discovery, characterization, and synthesis of RiPPs.

Present and future outlooks on environmental DNA-based methods for antibiotic discovery

Novel antibiotics are in constant demand to combat a global increase in antibiotic-resistant infections. Bacterial natural products have been a long-standing source of antibiotic compounds, and metagenomic mining of environmental DNA (eDNA) has increasingly provided new antibiotic leads. The metagenomic small-molecule discovery pipeline can be divided into three main steps: surveying eDNA, retrieving a sequence of interest, and accessing the encoded natural product. Improvements in sequencing technology, bioinformatic algorithms, and methods for converting biosynthetic gene clusters into small molecules are steadily increasing our ability to discover metagenomically encoded antibiotics. We predict that, over the next decade, ongoing technological improvements will dramatically increase the rate at which antibiotics are discovered from metagenomes.

Investigating and Optimizing the Lysate-Based Expression of Nonribosomal Peptide Synthetases Using a Reporter System

Lysate-based cell-free expression (CFE) systems are accessible platforms for expressing proteins that are difficult to synthesize in vivo, such as nonribosomal peptide synthetases (NRPSs). NRPSs are large (>100 kDa), modular enzyme complexes that synthesize bioactive peptide natural products. This synthetic process is analogous to transcription/translation (TX/TL) in lysates, resulting in potential resource competition between NRPS expression and NRPS activity in cell-free environments. Moreover, CFE conditions depend on the size and structure of the protein. Here, a reporter system for rapidly investigating and optimizing reaction environments for NRPS CFE is described. This strategy is demonstrated in E. coli lysate reactions using blue pigment synthetase A (BpsA), a model NRPS, carrying a C-terminal tetracysteine (TC) tag which forms a fluorescent complex with the biarsenical dye, FlAsH. A colorimetric assay was adapted for lysate reactions to detect the blue pigment product, indigoidine, of cell-free expressed BpsA-TC, confirming that the tagged enzyme is catalytically active. An optimized protocol for end point TC/FlAsH complex measurements in reactions enables quick comparisons of full-length BpsA-TC expressed under different reaction conditions, defining unique requirements for NRPS expression that are related to the protein's catalytic activity and size. Importantly, these protein-dependent CFE conditions enable higher indigoidine titer and improve the expression of other monomodular NRPSs. Notably, these conditions differ from those used for the expression of superfolder GFP (sfGFP), a common reporter for optimizing lysate-based CFE systems, indicating the necessity for tailored reporters to optimize expression for specific enzyme classes. The reporter system is anticipated to advance lysate-based CFE systems for complex enzyme synthesis, enabling natural product discovery.

Streptomyces cell-free systems for natural product discovery and engineering

Streptomyces bacteria are a major microbial source of natural products, which are encoded within so-called biosynthetic gene clusters (BGCs). This highlight discusses the emergence of native Streptomyces cell-free systems as a new tool to accelerate the study of the fundamental chemistry and biology of natural product biosynthesis from these bacteria. Cell-free systems provide a prototyping platform to study plug-and-play reactions in microscale reactions. So far, Streptomyces cell-free systems have been used to rapidly characterise gene expression regulation, access secondary metabolite biosynthetic enzymes, and catalyse cell-free transcription, translation, and biosynthesis of example natural products. With further progress, we anticipate the development of more complex systems to complement existing experimental tools for the discovery and engineering of natural product biosynthesis from Streptomyces and related high G + C (%) bacteria.

Toward the Heterologous Biosynthesis of Plant Natural Products: Gene Discovery and Characterization

Plant natural products (PNPs) represent a vast and diverse group of natural products, which have wide applications such as emulsifiers in cosmetics, sweeteners in foods, and active ingredients in medicines. Large-scale production of certain PNPs (e.g., artemisinin, taxol) has been implemented by reconstruction of biosynthetic pathways in heterologous hosts. However, unknown biosynthetic pathways greatly restrict wide applications of heterologous production of PNPs of interest. With the rapid development of sequencing and multiomics analysis technologies, huge amounts of omics data, i.e., genomics, transcriptomics, and proteomics, have been deposited in public databases, which is a precious resource for identification of the unknown biosynthetic pathway of PNPs. Herein, we have enumerated the approaches which have been widely used to screen candidate genes involved in the biosynthesis of PNPs of interest. We also discuss recent developments in the characterization of putative genes and elucidation of the complete biosynthetic pathway in heterologous hosts.

Biocatalytic synthesis of peptidic natural products and related analogues

Peptidic natural products (PNPs) represent a rich source of lead compounds for the discovery and development of therapeutic agents for the treatment of a variety of diseases. However, the chemical synthesis of PNPs with diverse modifications for drug research is often faced with significant challenges, including the unavailability of constituent nonproteinogenic amino acids, inefficient cyclization protocols, and poor compatibility with other functional groups. Advances in the understanding of PNP biosynthesis and biocatalysis provide a promising, sustainable alternative for the synthesis of these compounds and their analogues. Here we discuss current progress in using native and engineered biosynthetic enzymes for the production of both ribosomally and nonribosomally synthesized peptides. In addition, we highlight new in vitro and in vivo approaches for the generation and screening of PNP libraries.

A Streptomyces venezuelae Cell-Free Toolkit for Synthetic Biology

Prokaryotic cell-free coupled transcription–translation (TX-TL) systems are emerging as a powerful tool to examine natural product biosynthetic pathways in a test tube. The key advantages of this approach are the reduced experimental time scales and controlled reaction conditions. To realize this potential, it is essential to develop specialized cell-free systems in organisms enriched for biosynthetic gene clusters. This requires strong protein production and well-characterized synthetic biology tools. The Streptomyces genus is a major source of natural products. To study enzymes and pathways from Streptomyces, we originally developed a homologous Streptomyces cell-free system to provide a native protein folding environment, a high G+C (%) tRNA pool, and an active background metabolism. However, our initial yields were low (36 μg/mL) and showed a high level of batch-to-batch variation. Here, we present an updated high-yield and robust Streptomyces TX-TL protocol, reaching up to yields of 266 μg/mL of expressed recombinant protein. To complement this, we rapidly characterize a range of DNA parts with different reporters, express high G+C (%) biosynthetic genes, and demonstrate an initial proof of concept for combined transcription, translation, and biosynthesis of Streptomyces metabolic pathways in a single “one-pot” reaction.

Plant-Derived Cell-Free Biofactories for the Production of Secondary Metabolites

Cell-free expression systems enable the production of proteins and metabolites within a few hours or days. Removing the cellular context while maintaining the protein biosynthesis apparatus provides an open system that allows metabolic pathways to be installed and optimized by expressing different numbers and combinations of enzymes. This facilitates the synthesis of secondary metabolites that are difficult to produce in cell-based systems because they are toxic to the host cell or immediately converted into downstream products. Recently, we developed a cell-free lysate derived from tobacco BY-2 cell suspension cultures for the production of recombinant proteins. This system is remarkably productive, achieving yields of up to 3 mg/mL in a one-pot in vitro transcription-translation reaction and contains highly active energy and cofactor regeneration pathways. Here, we demonstrate for the first time that the BY-2 cell-free lysate also allows the efficient production of several classes of secondary metabolites. As case studies, we synthesized lycopene, indigoidine, betanin, and betaxanthins, which are useful in the food, cosmetic, textile, and pharmaceutical industries. Production was achieved by the co-expression of up to three metabolic enzymes. For all four products, we achieved medium to high yields. However, the yield of betanin (555 μg/mL) was outstanding, exceeding the level reported in yeast cells by a factor of more than 30. Our results show that the BY-2 cell-free lysate is suitable not only for the verification and optimization of metabolic pathways, but also for the efficient production of small to medium quantities of secondary metabolites.