Description

Background

Agriculture has always been the cornerstone of global food security and economic stability. As the world’ s population continues to grow, the demand for safe, sustainable, and efficient agricultural production is becoming increasingly urgent. However, bacterial plant diseases have emerged as one of the major factors limiting both crop yield and quality. Studies show that more than 200 bacterial pathogens worldwide can cause serious diseases in economically important crops, leading to tremendous yield losses and economic damage each year. Pathogens such as Xanthomonas, Pseudomonas, and Ralstonia infect crops including rice, tomato, citrus, and potato, and once outbreaks occur, they often result in large-scale yield reduction or even complete crop failure.

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At present, traditional control methods mainly rely on chemical bactericides and antibiotics, such as copper-based compounds and streptomycin. While these treatments can effectively suppress diseases in the short term, their long-term use brings multiple drawbacks:

Environmental pollution: Copper compounds are difficult to degrade in soil, leading to heavy metal accumulation that harms beneficial microorganisms and soil fauna. In addition, spraying chemical pesticides releases harmful substances into the air, water, and crops, posing risks to both ecosystems and food safety.

Antimicrobial resistance: The overuse of antibiotics and chemical agents accelerates the emergence of resistant bacterial strains, gradually reducing the effectiveness of disease control.

Food waste and health risks: Bacterial infections not only reduce crop yields but also cause visible blemishes on fruits and vegetables, lowering their market value and increasing waste during retail and consumption. Moreover, some preservatives and antimicrobial agents used in postharvest management may pose potential health risks to humans.

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In recent years, biological control methods—such as the application of antagonistic bacteria or beneficial microbial agents—have gained attention for their environmental safety. However, these methods often suffer from poor stability under field conditions, being highly affected by temperature, humidity, and microbial competition, which limits their large-scale application.

Against this backdrop, Phagri was developed. Based on synthetic biology and phage-inspired mechanisms, this project aims to create a biological pesticide capable of specifically recognizing and killing pathogenic bacteria, providing a precise, eco-friendly alternative for sustainable agricultural protection.

PhAgri

We have proposed an innovative solution: modifying E. coli MG1655 into a highly controllable “biological factory” for the large-scale production of phage-like particles. Our overall goal is to build a modular and programmable antibacterial platform. Through systematic engineering, we have achieved precise control over the entire chain from “production” to “attack”.

What are phage-like particles

Phage-like particles retain the key structures that allow T7 bacteriophages to recognize and invade bacteria, while removing their ability to replicate autonomously and lyse (break down) host cells. They act like a Trojan horse—capable of accurately delivering a “lethal payload” into target pathogenic bacteria, yet unable to self-replicate. This enables safe and controllable bactericidal effects.

How we use phage-like particles

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Precision Targeting: Controlled Delivery of Toxin Genes

We replaced the genome of wild-type T7 bacteriophages with our artificially designed toxin plasmid, formed as a multimeric DNA via rolling circle replication. This plasmid contains:

T7 packaging sequence: Ensures efficient replication and packaging of plasmid DNA into the phage head capsid.
Toxin gene MazF: A ribonuclease that cleaves mRNA, effectively blocking protein synthesis in target bacteria and causing their death.

The resulting phage-like particles deliver only the toxin gene upon infecting target bacteria. Since these particles lack any genes for phage replication or structural proteins, they complete their mission after successfully “killing” the target bacteria without producing offspring, fundamentally preventing uncontrolled self-replication.

Safe Production: Dual Safeguards for the Host Strain

To prevent toxin gene MazF expressing inthe host strain, we implemented a dual-safety strategy:

The antitoxin gene MazE is controlled by an arabinose-inducible promoter. Adding an inducer during fermentation continuously neutralizes the MazF toxin expressed from the plasmid.
Should the chassis organism escape during fermentation, its MazE gene cannot be expressed, leading to its destruction by the MazF toxin expressed from the plasmid.

These two systems collectively ensure the stability and safety of our “biological factory” during amplification and production of phage-like particles.

Controlled Production: Fragmentation and Induced Expression of the Phage Genome

To ensure the final product consists of pure phage-like particles rather than wild-type T7 phage contamination, we fragmented the engineered T7 phage genome and integrated it into the chassis organism genome.

We removed the T7 packaging sequence from the wild-type T7 genome, rendering it incapable of replication and packaging.

Simultaneously, T7 RNA polymerase (gp1) expression is controlled by an IPTG-inducible promoter. This ensures that phage-like particle synthesis only commences upon addition of the inducer IPTG, enabling precise, controllable production.

Expanding Targeting Range: Modular Tail Reprogramming

To synthesize diverse phage-like particles targeting pathogens beyond E. coli, we designed a modular tail replacement strategy. By replacing the natural T7 tail fiber gene with tail fiber genes from other phages, we can reprogram the targeting capability of phage-like particles like changing keys, enabling them to target multiple pathogens such as Pseudomonas syringae. This elevates our platform to a universal, programmable antimicrobial platform.

Advantages

Precise Targeting to Reduce Environmental Burden

By engineering the tail fiber proteins of phage-like particles, PhAgri achieves precise recognition and elimination of specific pathogenic bacteria (e.g., Pseudomonas syringae pv. tomato DC3000). This avoids the broad-spectrum toxicity of traditional chemical pesticides to beneficial organisms in soil and water, while effectively preventing the accumulation of heavy metals in soil caused by copper-based pesticides—thus reducing chemical damage to ecosystems at the source. Additionally, phage-like particles contain no self-replication genes, and their protein coats can be completely degraded in soil. This not only preserves soil microbial diversity but also helps beneficial soil bacteria become dominant species, further maintaining the ecological balance of farmland.

Empowering Farmers to Safeguard Food Security

Farmers are not only users of PhAgri but can also participate in its production and promotion. Through hierarchical training, marginal rural laborers such as women and the elderly can master simple operational procedures, which drives rural employment. Meanwhile, as a green biopesticide, the use of PhAgri significantly reduces pesticide residues in crops, enabling farmers to produce fruits and vegetables with “low residues and high quality.” This feature not only helps farmers meet the entry requirements of supermarkets and increase their income but also aligns with the demand for “safe and nutritious food” outlined in SDG 2 (“Zero Hunger”).

Global Adaptability to Practice Global Consensus

PhAgri’ s core goal of advancing the green transformation of agriculture is highly consistent with the initiative of the Food and Agriculture Organization (FAO) and the World Health Organization (WHO) to “gradually phase out highly hazardous pesticides.” At the international cooperation level, the project can leverage China-Africa Science and Technology Villages to promote mature “technology packages” (including formulation recipes and spraying methods) to agriculturally vulnerable countries such as Malawi and Ethiopia. For instance, to address the issues of low yields and weak technical capacity faced by smallholder farmers in Africa, PhAgri can lower adoption barriers through methods like controlled experiments in demonstration fields and free trials. This not only responds to the global call of SDG 2 (“Zero Hunger”) but also provides a practical case for international collaboration in advancing SDG 12 (“Responsible Consumption and Production”).

To be continued

In fact, our PhAgri has broader applications in agricultural production. Based on its specificity for pathogenic bacteria, we can modify its capsid proteins using phage display technology, such as by incorporating fluorescent proteins, to enable quantitative monitoring of pathogens. Additionally, since the obtained PLP (Phage-Like Particles) can package different DNA internally, it also possesses the ability to amplify signals. The high sensitivity and specificity of PLP make it a promising candidate for an excellent pathogen detector, allowing for early problem identification before initial symptoms appear. Furthermore, based on protein structure prediction, we anticipate the future possibility of artificially designing phages to address the current challenges in phage isolation, thereby providing solutions for issues potentially caused by bacteria.