Synthetic Biology and Its Applications in Phage Research

1. The development of synthetic biology

The source divides the development of synthetic biology into three periods: a foundational period in which classic experiments and the field’s culture emerged; an intermediate period of expansion in which engineering lagged behind; and an era of accelerating innovation in which new technologies enabled practical applications in biotechnology and medicine.

The original article refers to “Figure 1: A brief history of synthetic biology” [1], but no corresponding image is included in the archived article body.

2. Applications in phage research

Improving phage activity

Phages engineered to express enzymes that degrade biofilm matrix can penetrate and disrupt biofilms more effectively in experimental systems. The source describes a T7 phage expressing dispersin B (DspB), which performed approximately three times better against an experimental Escherichia coli biofilm than the comparator lacking DspB.

The plant pathogen Erwinia amylovora produces a capsule that can obstruct phage activity. Introducing the capsule depolymerase gene dpoL1-C from phage L1 into the unrelated phage Y2 generated larger, clearer plaques. Despite a lower burst size, the engineered phage produced an approximately three-log reduction in bacteria after 24 hours compared with wild-type phage in the experiment described. Results from experimental flower infections were consistent with the antibacterial findings. These examples illustrate how engineering phages to encode hydrolases or depolymerases can improve particular laboratory properties.

Altering host range

Phage cocktails are often used to broaden coverage because individual phages are host-specific. Cocktails may need updating as bacterial populations change, creating practical and regulatory challenges. Host-range engineering offers a possible way to modify established phage scaffolds, although the safety and effectiveness of each resulting product still require evaluation.

Ando and colleagues constructed synthetic T7-like phages with altered host ranges. In this group, host specificity is strongly influenced by tail structures encoded by gene 17. Exchanging gene 17 with homologues from several related phages produced predictable changes. Creating a hybrid between T7 and the Klebsiella phage K11, however, required replacement of all three tail genes—11, 12 and 17—with their K11 counterparts, a difficult task using conventional allelic exchange.

This strategy depends on exchanging components among known phages and is therefore constrained by the availability of characterized, sequenced phages. High-throughput methods for adapting host range could be valuable for future phage therapy research.

Converting temperate phages into lytic phages

Temperate phages can integrate into bacterial genomes and may carry undesirable genes, so they are generally avoided in conventional therapeutic selection. For some bacteria, however, suitable naturally lytic phages are difficult to isolate, motivating research into engineered alternatives.

The source describes work by Kilcher and colleagues using the Listeria phage P335 as a scaffold. Removal of its main repressor generated a strictly lytic mutant, and expression of a second endolysin further increased lytic activity. In the reported experiments, the resulting phage did not lysogenize Listeria, killed the bacteria effectively and reduced the emergence of resistance.

Engineering antibacterial lysins

Briers and colleagues developed synthetic phage lysins known as Artilysins. These combine lysins with peptides designed to disrupt the Gram-negative outer membrane, allowing activity without relying on active transport. The constructs described used lipopolysaccharide-destabilizing peptides fused to selected endolysins.

The source reports that the most effective constructs reduced Pseudomonas aeruginosa, Acinetobacter baumannii, E. coli and Salmonella Typhimurium counts by four to five orders of magnitude, and stationary-phase A. baumannii by eight orders of magnitude, under the cited experimental conditions [2].

Outlook

Increasing antibiotic resistance drives the search for new antibacterial agents. Phage-based approaches are promising but face constraints including narrow host range, bacterial resistance to phages, manufacturing cost and dosing or delivery challenges. Advances in synthetic genome assembly and viral genome engineering may help address these limitations. Engineered phages could also create intellectual-property opportunities and encourage pharmaceutical development.

Related technologies are being investigated for diagnostic or therapeutic nanocarriers with improved tissue penetration and payload capacity, including potential applications in cancer and other diseases [3]. These are research directions, not claims of established clinical efficacy.

References

1. Cameron DE, Bashor CJ, Collins JJ. A brief history of synthetic biology. Nature Reviews Microbiology. 2014;12(5):381–390.
2. Lemire S, Yehl KM, Lu TK. Phage-Based Applications in Synthetic Biology. Annual Review of Virology. 2018;5(1):453–476.
3. Barbu EM, Cady KC, Hubby B. Phage Therapy in the Era of Synthetic Biology. Cold Spring Harbor Perspectives in Biology. 2016;8(10).