In the relentless quest to harness nature’s biochemical arsenal, researchers have pushed the boundaries of microbial engineering, uncovering novel strategies for scalable production of valuable secondary metabolites. These compounds—ranging from antibiotics to anticancer agents—are vital to medicine, agriculture, and biotechnology. Among the microbial workhorses, species of the genus Streptomyces stand out as prolific producers of these bioactive molecules. However, translating the rich secondary metabolite profiles of Streptomyces strains into viable industrial processes has posed significant challenges. Addressing these limitations, a groundbreaking study now introduces an innovative plug-and-play system that fundamentally reshapes the landscape of microbial metabolite production, promising rapid scale-up and unprecedented control.
At the core of the breakthrough lies the engineering of a versatile artificial control system, termed Streptomyces multiplexed artificial control system (SMARTS). This system leverages the enigmatic language of quorum sensing—cellular communication via chemical signals—interlinking bacterial population dynamics with gene expression regulation. While Streptomyces species exhibit complex quorum sensing systems, the new research reveals that diverse quorum-sensing receptors within this genus surprisingly converge on recognizing identical DNA-binding sites. This insight serves as a linchpin for constructing a synthetic promoter responsive to multiple quorum-sensing signals, enabling a universally applicable regulatory element across a broad spectrum of Streptomyces strains.
The synthetic promoter acts as a switchboard, translating the fluctuating presence of chemical signals in the microbial milieu into precise transcriptional responses. However, natural quorum sensing signals tend to be transient and inherently noisy, complicating stable genetic circuit implementation. To transcend this noise barrier, the researchers integrated the promoter with a genetic stabilizer and a sophisticated multiplexer module. Together, these elements convert ephemeral quorum signals into stable, multiplexed outputs that can be finely tuned in strength, effectively enabling graded, multiplexed control over gene expression within the cell.
The architectural elegance of the SMARTS system lies not only in its modularity but in its adaptability. It permits simultaneous control over multiple genetic targets, orchestrating complex metabolic pathways in a plug-and-play format. This modularity significantly simplifies the strain engineering pipeline, reducing the trial-and-error bottlenecks previously encountered when attempting to optimize diverse secondary metabolite biosynthetic routes across distinct Streptomyces species.
To demonstrate the system’s power and flexibility, the researchers engineered two distinct Streptomyces strains tailored for distinct applications. The first was a redesigned native Streptomyces avermitilis, optimized for specialized production of baiweimectin, a potent nematicide with agricultural importance. By fine-tuning the genetic circuitry with SMARTS, this strain achieved remarkable production titers. Even more impressively, the baiweimectin-producing S. avermitilis strain was successfully scaled up to an industrial fermenter of 120 cubic meters—the magnitude necessary for commercial exploitation—yielding a titer of 8.4 grams per liter. Such scale and yield signify a significant leap forward, bridging the oft-dreaded gap between laboratory bench success and industrial viability.
The second application spotlighted the capacity for de novo programming: the researchers introduced the SMARTS system into Streptomyces venezuelae for heterologous production of epidoxorubicin, a semisynthesized antitumor agent. This demonstration of precise, multiplexed control over a complex biosynthetic pathway in a heterologous host underscores the system’s versatility and its potential in drug development pipelines, where heterologous expression is often crucial for accessing compounds from uncultivable or genetically intractable organisms.
The implications of this SMARTS platform extend well beyond the strains tested. Secondary metabolites from Streptomyces species encompass a vast chemical repertoire, including antibiotics like streptomycin and tetracycline, immunosuppressants, and anticancer agents. Historically, these secondary metabolites are expressed under tightly regulated, complex developmental programs often dependent on specific growth phases and environmental cues. Dissecting and manipulating these native regulatory networks has been notoriously difficult. The SMARTS system circumvents these limitations by offering a programmable regulatory framework decoupled from native complexities, yet fully compatible with the host’s molecular machinery.
Mechanistically, the SMARTS framework hinges on exploiting the shared DNA-binding motif recognized by various quorum-sensing receptors. Typically, quorum sensing is implemented via small signaling molecules like γ-butyrolactones, which bind to cognate receptor proteins that act as transcriptional regulators. By identifying that different receptors, even from phylogenetically distant Streptomyces strains, bind an identical promoter sequence, the researchers could engineer a universal quorum-sensing responsive element. This universal promoter enables cross-strain functionality, eliminating the need for bespoke promoter construction for each species or strain and fostering broad applicability.
The stabilizer component within SMARTS functions as a genetic memory device, mitigating the temporal fluctuations characteristic of native quorum-sensing signals. This element anchors transient activation into enduring output states, thereby enhancing metabolic output stability and predictability—critical prerequisites for industrial fermentation. On the other hand, the multiplexer module empowers the system to manage multiple input signals and mediate diverse outputs, akin to an electronic multiplexer. This versatility allows the design of complex genetic programs that can control multiple metabolic nodes simultaneously, optimizing flux through secondary metabolite biosynthetic pathways.
From an industrial bioprocessing perspective, the successful demonstration of SMARTS at a 120-m³ scale is particularly compelling. Scale-up often exposes limitations not apparent at lab or pilot scales, including instability of genetic modifications, metabolic burden, and inconsistent metabolite titers. The durability of the SMARTS-based S. avermitilis strain in these large—a step not just of scale but also of regulatory complexity—indicates a new paradigm where programmable artificial control circuits can maintain robust performance amid industrial constraints.
Moreover, the platform’s plug-and-play nature offers substantial time and cost savings. Conventionally, the development of optimized production strains involves laborious, iterative genetic engineering cycles specific to each product and host strain. SMARTS cuts through this bottleneck by allowing rapid assembly and deployment of multiplexed, quorum sensing–responsive circuits. This accelerates strain development timelines, enabling faster bench-to-factory transitions.
In practical terms, the ramifications of this technology span multiple sectors. For agriculture, where sustainable pest control agents like nematicides are urgently needed, the ability to upregulate bioactive compound synthesis reproducibly and at scale can significantly impact crop protection strategies. In medicine, scalable production of complex drugs, particularly those requiring complex biosynthetic machinery like epidoxorubicin, can facilitate more affordable and accessible therapies. The biotechnology sector at large stands to gain a robust chassis for both natural product pathway discovery and commercial manufacturing.
Future prospects for the SMARTS system are immense. Expanding the repertoire of quorum sensing receptors and refining multiplexing logic could allow even finer control, including conditional, programmable switches responsive to environmental or metabolic cues. Additionally, integration with high-throughput screening and machine learning-driven design could automate and optimize genetic programs further, harnessing the full potential of synthetic biology for microbial cell factories.
Ultimately, this innovative research embodies the marriage of synthetic biology, microbial engineering, and industrial biotechnology, leveraging fundamental discoveries in bacterial communication to transform secondary metabolite production. The development and scalable validation of SMARTS establish it as a versatile platform capable of catalyzing the next generation of microbial production systems, propelling natural product biosynthesis into an era of programmable, predictable, and economically feasible manufacturing.
As industries grapple with the urgent need for novel bioactive compounds, sustainable production methods, and the shrinking discovery pipeline of natural products, advances such as SMARTS provide a beacon of hope. By enabling multiplexed, stable, and strain-agnostic control of complex biosynthetic pathways, this platform not only accelerates the pace of innovation but does so on an industrial scale, with clear implications for global health, agriculture, and bioeconomy.
This work sets a new standard for how microbial secondary metabolite production can be engineered, scaled, and commercialized. It paves the way for programmable cell factories that are no longer limited by the idiosyncrasies of individual strains or metabolic pathways but are instead governed by precise, multiplexed genetic circuits that translate the language of microbes into human-scale bioengineering solutions.
Subject of Research:
Development of a versatile, quorum-sensing-based artificial control system (SMARTS) for scalable and multiplexed secondary metabolite production in Streptomyces species.
Article Title:
Scalable secondary metabolite production in Streptomyces using a plug-and-play system
Article References:
Yang, B., Li, Z., Zhang, J. et al. Scalable secondary metabolite production in Streptomyces using a plug-and-play system. Nat Biotechnol (2025). https://doi.org/10.1038/s41587-025-02762-1
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