Phage-Based Applications in Synthetic Biology
Diseases are crazy dangerous; I think that has become very obvious to everyone now with Covid-19 killing so many people. Expect it was so much worse back in the day, not just talking about the black plague but a simple paper cut could be a death sentence. Bacteria are killers, until only recently we got the upper hand on them with the discovery of penicillin. But before humans became bacteria’s main threat, there was an efficient bacteria-killing machine known as Phages. The full scientific name being Bacteriophage, these unique creatures have massive potential in the field of synthetic biology.
Ground Zero
So to start we need to know a little about Bacteriophage because without a proper understanding to use as a base, you will get lost reading this article.
A bacteriophage is a type of virus that kills bacteria. With the word “bacteriophage” itself meaning “bacteria eater” most phages range in size from 24–200 nm in length. The bacteriophage structure has a polyhedral head where the DNA is stored, a collar attached to a short neck-like structure and a helical tail which looks like legs. The craziest part is that they’re located everywhere bacteria can exist including, in the soil, deep within the earth’s crust, inside plants and animals, and even in the oceans.
Bacteriophages, when first discovered were taken with much controversy as being super common and having unknown biological properties not seen before. Eventually, we found out how groundbreaking and cool they were. With it being just over 100 years since it was discovered, leaving much-untapped potential. What can phages do?
Phage Therapy
Phage therapy has tons of applications. As with the surfacing of new and more lethal antibiotic-resistant bacteria being seen, worldwide, phage therapy has become more in demand. With phage therapy use natural phages as most bacteria aren’t immune to phages. Plus those bacteria that are immune to phages, you can use the help of genetic engineering to get around that problem.
Besides phages being an efficient bacteria killing machine, scientists are finding novel ways to use them to vaccinate people! You can edit them to display antigens that can help immunize you. Another application is using phages as biosensors. One of the coolest possible applications of phages is using them to deliver cancer medication without damaging other healthy cells, like traditional chemotherapy.
Gene Editing Phages
Even though phages in nature already can be used for many therapeutic purposes, with gene editing we can make them more efficient and diverse in applications. One way we can genetically engineer phages is through homologous recombination. Where take a heterologous segment of DNA and recombine it with the phage genome at sites of homology within a bacterial host. The efficiency of recombination is very low even when done perfectly. So a screening method is necessary to identify recombinant phages, which can be done in many ways.
Now that we know how to genetically engineer the phages, we now need to start producing them rapidly. One method is through using Yeast for in vitro phage genome assembly. Which is both efficient at assembling the new phages but also prevents any toxins from altering phage replication. With the process of transformation-associated recombination (TAR) cloning, we can start the production of recombinant phages.
Applications of Genetically Engineered Phages
Using genetically engineered phages further enhances the capability of phage therapy. With the use of those phages being worked on in many laboratories from testing, altering and more testing trying to maximize phage therapy. Leaving nothing about the phage form being enhanced, replaced with new mechanisms to even completely removed certain features in their genome. So with all that being said, what is possible with the help of synthetic biology?
Unlimited Host Range
Phages in nature typically only attack a select range of bacteria species and strains within those species. Which can limit them in many use cases, in nature, it would be fine. However, in a lab, it would result in tedious testing to find the correct group of phages for the job. Alternatively, we can make synthetic phages which can be genetically modified to have an expansive range of hosts. This is possible by swapping genomic segments of the tail fibre. Several studies demonstrating a swap of the tail fibre of two different phages also outturn a swap in the host range. Other methods include fusing a receptor-binding domain to capsid proteins of different phages. With all these innovative methods, we can genetically modify phages to have a diverse range of hosts.
Delivering Antimicrobials
Phages are almost like homing missiles which can target and eliminate any target, in other words, the bacteria they are given. Their unique targeting ability opens up a whole bunch of possibilities for targeted delivery of antimicrobials. Using phages as targeted drug carriers to help in eradicating a certain group of bacteria. The way they achieved this was by genetically modifying two things. First, they made a synthetic coat protein for the phage that carried the group of bacteria’s peptides, and by attaching antibodies to the phage were able to bind to the bacteria and deliver the antimicrobials.
Vaccines
Another unique characteristic of phages is their ability to link genotype and phenotype, making them a very valuable asset. This ability can be used flawlessly for vaccination and antibody development. Phages are best suited for a DNA or RNA-based vaccine delivery method. Especially with the addition of the phage capsid, which is the perfect way to transfer nucleic acids. Furthermore, some phage capsid proteins can cause an immune response not further requiring any form of an adjuvant to support. Turning our phage into the perfect package for a vaccine.
Phages as Sensors
This might sound like a strange application of phages, but as it turns out, phages can be made into a biosensor. Sensors only have two main functions: one is some recognition element to recognize targets. The second thing a sensor needs is a mechanism for reporting when the recognition element detects the target.
Phages can be genetically engineered into a biosensor, as there are already receptor-binding proteins on the phages that are used to detect targets, in this case, bacteria. Bacteriophages already being incredible at identifying their targets, already made them strong candidates as biosensors. The only issue is that it would be very difficult and time-consuming to recognize when the phage had got the right target.
Deploying Targeted CRISPR Editing
One of the coolest applications of bacteriophages is they have the potential to allow for extremely precise CRISPR Editing! For those who don’t know what CRISPR is, it can essentially edit the genome of any living thing! Therefore, to put it more simply, it’s a ctrl+f and Delete protein. One of the most common CRISPR proteins is Cas9. CRISPR editing can inactivate or modify any gene in a bacteria. Testing out its possibilities, they genetically modified a phage to carry CRISPR; more specifically Cas3 protein. They would use that bacteriophage to hunt a group of bacteria, upon infection of the synthetic phage they injected CRISPR activating the endogenous Cas3 protein to processively digest the chromosomal DNA of the bacteria. The research concluded that the genetically modified phage was a more efficient bacteria killer than, its counterpart found in nature.
Bacteriophages have an almost limitless potential in what we can do with it, even though it might sound cliche. So research yourself, comment on what you found, and clap if you think this article taught you something.
