Synthetic Inducible Regulatory Systems Optimized for the Modulation of Secondary Metabolite Production in Streptomyces

A Simple and Effective Strategy for the Development of Robust Promoter-Centric Gene Expression Tools

Promoter-centric genetic tools play a crucial role in controlling gene expression for various applications, such as strain engineering and synthetic biology studies. Hence, a critical need persists for the development of robust gene expression tools. Streptomyces are well-known prolific producers of natural products and exceptional surrogate hosts for the production of high-value chemical compounds and enzymes. In this study, we reported a straightforward and effective strategy for the creation of potent gene expression tools. This was primarily achieved by introducing an additional -35-like motif upstream of the original -35 region of the promoter, coupled with the integration of a palindromic cis-element into the 5'-UTR region. This approach has generated a collection of robust constitutive and inducible gene expression tools tailored for Streptomyces. Of particular note, the fully activated oxytetracycline-inducible gene expression system containing an engineered kasOp* promoter (OK) exhibited nearly an order of magnitude greater activity compared to the well-established high-strength promoter kasOp* under the tested conditions, establishing itself as a powerful gene expression system for Streptomyces. This strategy is expected to be applicable in modifying various other promoters to acquire robust gene expression tools, as evidenced by the enhancement observed in the other two promoters, PL and P21 in this study. Moreover, the effectiveness of these tools has been demonstrated through the augmented production of transglutaminase and daptomycin. The gene expression tools established in this study, alongside those anticipated in forthcoming research, are positioned to markedly advance pathway engineering and synthetic biology investigations in Streptomyces and other microbial strains.

Promoter engineering of natural product biosynthetic gene clusters in actinomycetes: concepts and applications

Covering 2011 to 2022Low titers of natural products in laboratory culture or fermentation conditions have been one of the challenging issues in natural products research. Many natural product biosynthetic gene clusters (BGCs) are also transcriptionally silent in laboratory culture conditions, making it challenging to characterize the structures and activities of their metabolites. Promoter engineering offers a potential solution to this problem by providing tools for transcriptional activation or optimization of biosynthetic genes. In this review, we summarize the 10 years of progress in promoter engineering approaches in natural products research focusing on the most metabolically talented group of bacteria actinomycetes.

Heterologous overproduction of oviedomycin by refactoring biosynthetic gene cluster and metabolic engineering of host strain Streptomyces coelicolor

BACKGROUND

Oviedomycin is one among several polyketides known for their potential as anticancer agents. The biosynthetic gene cluster (BGC) for oviedomycin is primarily found in Streptomyces antibioticus. However, because this BGC is usually inactive under normal laboratory conditions, it is necessary to employ systematic metabolic engineering methods, such as heterologous expression, refactoring of BGCs, and optimization of precursor biosynthesis, to allow efficient production of these compounds.

RESULTS

Oviedomycin BGC was captured from the genome of Streptomyces antibioticus by a newly constructed plasmid, pCBA, and conjugated into the heterologous strain, S. coelicolor M1152. To increase the production of oviedomycin, clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) system was utilized in an in vitro setting to refactor the native promoters within the ovm BGC. The target promoters of refactoring were selected based on examination of factors such as transcription levels and metabolite profiling. Furthermore, genome-scale metabolic simulation was applied to find overexpression targets that could enhance the biosynthesis of precursors or cofactors related to oviedomycin production. The combined approach led to a significant increase in oviedomycin production, reaching up to 670 mg/L, which is the highest titer reported to date. This demonstrates the potential of the approach undertaken in this study.

CONCLUSIONS

The metabolic engineering approach used in this study led to the successful production of a valuable polyketide, oviedomycin, via BGC cloning, promoter refactoring, and gene manipulation of host metabolism aided by genome-scale metabolic simulation. This approach can be also useful for the efficient production of other secondary molecules encoded by 'silent' BGCs.

Novel switchable ECF sigma factor transcription system for improving thaxtomin A production in Streptomyces

The application of the valuable natural product thaxtomin A, a potent bioherbicide from the potato scab pathogenic Streptomyces strains, has been greatly hindered by the low yields from its native producers. Here, we developed an orthogonal transcription system, leveraging extra-cytoplasmic function (ECF) sigma (σ) factor 17 (ECF17) and its cognate promoter P_ecf17, to express the thaxtomin gene cluster and improve the production of thaxtomin A. The minimal P_ecf17 promoter was determined, and a P_ecf17 promoter library with a wide range of strengths was constructed. Furthermore, a cumate inducible system was developed for precise temporal control of the ECF17 transcription system in S. venezuelae ISP5230. Theoretically, the switchable ECF17 transcription system could reduce the unwanted influences from host and alleviate the burdens introduced by overexpression of heterologous genes. The yield of thaxtomin A was significantly improved to 202.1 ± 15.3 μ g/mL using the switchable ECF17 transcription system for heterologous expression of the thaxtomin gene cluster in S. venezuelae ISP5230. Besides, the applicability of this transcription system was also tested in Streptomyces albus J1074, and the titer of thaxtomin A was raised to as high as 239.3 ± 30.6 μg/mL. Therefore, the inducible ECF17 transcription system could serve as a complement of the generally used transcription systems based on strong native constitutive promoters and housekeeping σ factors for the heterologous expression of valuable products in diverse Streptomyces hosts.

ClpP inhibitors are produced by a widespread family of bacterial gene clusters

The caseinolytic protease (ClpP) is part of a highly conserved proteolytic complex whose disruption can lead to antibacterial activity but for which few specific inhibitors have been discovered. Specialized metabolites produced by bacteria have been shaped by evolution for specific functions, making them a potential source of selective ClpP inhibitors. Here, we describe a target-directed genome mining strategy for discovering ClpP-interacting compounds by searching for biosynthetic gene clusters that contain duplicated copies of ClpP as putative antibiotic resistance genes. We identify a widespread family of ClpP-associated clusters that are known to produce pyrrolizidine alkaloids but whose connection to ClpP has never been made. We show that previously characterized molecules do not affect ClpP function but are shunt metabolites derived from the genuine product of these gene clusters, a reactive covalent ClpP inhibitor. Focusing on one such cryptic gene cluster from Streptomyces cattleya, we identify the relevant inhibitor, which we name clipibicyclene, and show that it potently and selectively inactivates ClpP. Finally, we solve the crystal structure of clipibicyclene-modified Escherichia coli ClpP. Clipibicyclene's discovery reveals the authentic function of a family of natural products whose specificity for ClpP and abundance in nature illuminate the role of eco-evolutionary forces during bacterial competition.

A Self-Sustained System Spanning the Primary and Secondary Metabolism Stages to Boost the Productivity of Streptomyces

Streptomyces species possess strong secondary metabolism, the switches of which from the primary metabolism are complex and thus a challenge to holistically optimize their productivities. To avoid the complex switches and to reduce the limitations of different metabolic stages on the synthesis of metabolites, we designed a Streptomyces self-sustained system (StSS) that contains two functional modules, the primary metabolism module (PM) and the secondary metabolism module (SM). The PM includes endogenous housekeeping sigma factor σ^hrdB and σ^hrdB-dependent promoters, which are used to express target genes in the primary metabolism phase. SM consists of the expression cassette of σ^hrdB under the control of a secondary metabolism promoter, which maintains continuous activity of the σ^hrdB-dependent promoters in the secondary metabolism phase. As a proof-of-principle, the StSS was used to boost the production of some non-toxic metabolites, including indigoidine, undecylprodigiosin (UDP), ergothioneine, and avermectin, in Streptomyces. All these metabolites can undergo a continuous production process spanning the primary and secondary metabolism stages instead of being limited to a specific stage. Scale-up of UDP fermentation in a 4 L fermentor indicated that the StSS is a stable and robust system, the titer of which was enhanced to 1.1 g/L, the highest at present. This study demonstrated that the StSS is a simple but powerful strategy to rationally engineer Streptomyces cell factories for the efficient production of non-toxic metabolites via reconstructing the relationships between primary and secondary metabolism.

Artificial Transcription Factors for Tuneable Gene Expression in Pichia pastoris

The non-conventional yeast Pichia pastoris (syn. Komagataella phaffii) has become a powerful eukaryotic expression platform for biopharmaceutical and biotechnological applications on both laboratory and industrial scales. Despite the fundamental role that artificial transcription factors (ATFs) play in the orthogonal control of gene expression in synthetic biology, a limited number of ATFs are available for P. pastoris. To establish orthogonal regulators for use in P. pastoris, we characterized ATFs derived from Arabidopsis TFs. The plant-derived ATFs contain the binding domain of TFs from the plant Arabidopsis thaliana, in combination with the activation domains of yeast GAL4 and plant EDLL and a synthetic promoter harboring the cognate cis-regulatory motifs. Chromosomally integrated ATFs and their binding sites (ATF/BSs) resulted in a wide spectrum of inducible transcriptional outputs in P. pastoris, ranging from as low as 1- to as high as ∼63-fold induction with only small growth defects. We demonstrated the application of ATF/BSs by generating P. pastoris cells that produce β-carotene. Notably, the productivity of β-carotene in P. pastoris was ∼4.8-fold higher than that in S. cerevisiae, reaching ∼59% of the β-carotene productivity obtained in a S. cerevisiae strain optimized for the production of the β-carotene precursor, farnesyl diphosphate, by rewiring the endogenous metabolic pathways using plant-derived ATF/BSs. Our data suggest that plant-derived regulators have a high degree of transferability from S. cerevisiae to P. pastoris. The plant-derived ATFs, together with their cognate binding sites, powerfully increase the repertoire of transcriptional regulatory modules for the tuning of protein expression levels required in metabolic engineering or synthetic biology in P. pastoris.

Synthetic Cellobiose-Inducible Regulatory Systems Allow Tight and Dynamic Controls of Gene Expression in Streptomyces

Precise control of microbial gene expression is crucial for synthetic biotechnological applications. This is particularly true for the bacterial genus Streptomyces, major producers of diverse natural products including many antibiotics. Although a plethora of genetic tools have been developed for Streptomyces, there is still an urgent need for effective gene induction systems. We herein created two novel cellobiose-inducible regulatory systems referred to as Cel-RS1 and Cel-RS2. The regulatory systems are based upon the well-characterized repressor/operator pair CebR/cebO from Streptomyces scabies and the well-defined constitutive kasO* promoter. Both Cel-RS1 and Cel-RS2 exhibit a high level of induced reporter activity and virtually no leaky expression in three model Streptomyces species, which are commonly used as surrogate hosts for expression of natural product biosynthetic gene clusters. Cel-RS2 has been proven successful for programmable control of gene expression and controllable production of specialized metabolites in multiple Streptomyces species. The strategy can be used to expand the toolkit of inducible regulatory systems that will be broadly applicable to various Streptomyces.

The Design-Build-Test-Learn cycle for metabolic engineering of Streptomycetes

Streptomycetes are producers of a wide range of specialized metabolites of great medicinal and industrial importance, such as antibiotics, antifungals, or pesticides. Having been the drivers of the golden age of antibiotics in the 1950s and 1960s, technological advancements over the last two decades have revealed that very little of their biosynthetic potential has been exploited so far. Given the great need for new antibiotics due to the emerging antimicrobial resistance crisis, as well as the urgent need for sustainable biobased production of complex molecules, there is a great renewed interest in exploring and engineering the biosynthetic potential of streptomycetes. Here, we describe the Design-Build-Test-Learn (DBTL) cycle for metabolic engineering experiments in streptomycetes and how it can be used for the discovery and production of novel specialized metabolites.

Synthetic biology-inspired strategies and tools for engineering of microbial natural product biosynthetic pathways

Microbial-derived natural products (NPs) and their derivative products are of great importance and used widely in many fields, especially in pharmaceutical industries. However, there is an immediate need to establish innovative approaches, strategies, and techniques to discover new NPs with novel or enhanced biological properties, due to the less productivity and higher cost on traditional drug discovery pipelines from natural bioresources. Revealing of untapped microbial cryptic biosynthetic gene clusters (BGCs) using DNA sequencing technology and bioinformatics tools makes genome mining possible for NP discovery from microorganisms. Meanwhile, new approaches and strategies in the area of synthetic biology offer great potentials for generation of new NPs by engineering or creating synthetic systems with improved and desired functions. Development of approaches, strategies and tools in synthetic biology can facilitate not only exploration and enhancement in supply, and also in the structural diversification of NPs. Here, we discussed recent advances in synthetic biology-inspired strategies, including bioinformatics and genetic engineering tools and approaches for identification, cloning, editing/refactoring of candidate biosynthetic pathways, construction of heterologous expression hosts, fitness optimization between target pathways and hosts and detection of NP production.

Recent advances in heterologous expression of natural product biosynthetic gene clusters in Streptomyces hosts

The heterologous expression of natural product biosynthetic gene clusters (BGCs) has traditionally been used as a genetic platform to link various natural product chemotypes to their corresponding genotypes. In recent years, heterologous expression has played an increasing role in natural products research with the advances in sequencing technologies and bioinformatics tools that allow for the rapid and systematic identification of known and cryptic BGCs from a large number of microbial genome sequences. The advances in synthetic biology have also facilitated the process of heterologous expression by providing tools for rapid cloning and engineering of BGCs to improve production yield or to activate silent BGCs. This paper summarizes the recent progress in the cloning and engineering of natural product BGCs and highlights recent examples of the heterologous expression of both known and cryptic BGCs in Streptomyces hosts, which will continue to play a pivotal role in genomics-driven natural product research.

An Update on Molecular Tools for Genetic Engineering of Actinomycetes-The Source of Important Antibiotics and Other Valuable Compounds

The first antibiotic-producing actinomycete (Streptomyces antibioticus) was described by Waksman and Woodruff in 1940. This discovery initiated the "actinomycetes era", in which several species were identified and demonstrated to be a great source of bioactive compounds. However, the remarkable group of microorganisms and their potential for the production of bioactive agents were only partially exploited. This is caused by the fact that the growth of many actinomycetes cannot be reproduced on artificial media at laboratory conditions. In addition, sequencing, genome mining and bioactivity screening disclosed that numerous biosynthetic gene clusters (BGCs), encoded in actinomycetes genomes are not expressed and thus, the respective potential products remain uncharacterized. Therefore, a lot of effort was put into the development of technologies that facilitate the access to actinomycetes genomes and activation of their biosynthetic pathways. In this review, we mainly focus on molecular tools and methods for genetic engineering of actinomycetes that have emerged in the field in the past five years (2015-2020). In addition, we highlight examples of successful application of the recently developed technologies in genetic engineering of actinomycetes for activation and/or improvement of the biosynthesis of secondary metabolites.

Recent Advances in Synthetic Biology Approaches to Optimize Production of Bioactive Natural Products in Actinobacteria

Actinobacteria represent one of the most fertile sources for the discovery and development of natural products (NPs) with medicinal and industrial importance. However, production titers of actinobacterial NPs are usually low and require optimization for compound characterization and/or industrial production. In recent years, a wide variety of novel enabling technologies for engineering actinobacteria have been developed, which have greatly facilitated the optimization of NPs biosynthesis. In this review, we summarize the recent advances of synthetic biology approaches for overproducing desired drugs, as well as for the discovery of novel NPs in actinobacteria, including dynamic metabolic regulation based on metabolite-responsive promoters or biosensors, multi-copy chromosomal integration of target biosynthetic gene clusters (BGCs), promoter engineering-mediated rational BGC refactoring, and construction of genome-minimized Streptomyces hosts. Integrated with metabolic engineering strategies developed previously, these novel enabling technologies promise to facilitate industrial strain improvement process and genome mining studies for years to come.