Engineering phage ΦX174's genome: a recap of November's PHAVES talk

This month, we hosted Dr. Paul Jaschke, Assistant Professor at Macquarie University, Sydney, Australia, and CSO of Hyperdrive Science for our November episode of PHAVES; check out the recap below!

PHAVES 10

Learning how to engineer genomes by building phage

YouTube video of PHAVES 10 (1:00:24)

Highlights of Paul’s talk

• Throughout his career, Paul has extensively studied a phage that belongs to the Microviridae family known as ΦX174. This phage is known to infect specific strains of Escherichia coli and Salmonella spp.
• Interestingly, throughout its infection process, ΦX174 creates a protein known as ‘Protein E’ which is an antibiotic-like lysis protein which disrupts peptidoglycan synthesis, which may be of interest from a therapeutic point of view.
• However, Paul’s work (at Macquarie University, Sydney, Australia) has focused on the genome of ΦX174, which is a circular ssDNA genome with extensive gene overlap. The overlap allows the 11 genes to only span across 5,386 bp. Does this overlap account for a message from extra-terrestrial intelligence? Unfortunately, probably not. However, importantly, a genome size >5kb does result in a lowered infectivity rate!
• Due to the structure of the ΦX174 genome, Paul and his team are interested in using this phage for synthetic genomics, which is the “extensive and intentional genetic modification of a replicating system for a specific purpose”. Why phage genomes for synthetic genomics?
• Phages are self-contained genetic programs with a constant operating system, therefore easier to tell if changes affect points of the phage lifecycle
• Phage lifecycles share characteristics such as DNA replication with other self-replicating systems
• Understanding how to engineer phage genomes may help accelerate them as next generation antimicrobials
• However, as mentioned, ΦX174 has gene overlaps, therefore, Paul begun by decompressing the genome of ΦX174 to remove all overlaps. Characterisation of decompressed ΦX174 found that it had smaller plaque sizes, smaller burst size, poor attachment and a downregulation of two proteins involved in scaffolding and replication in comparison to wild type ΦX174. Despite this, CryoTEM revealed that the structure of decompressed ΦX174 was indistinguishable from wild type ΦX174, and decompressed ΦX174 lysed cells at a similar efficiency in vitro at a higher MOI. This highlights the important trade-offs between removing overlaps and phage fitness.
• Paul finished up by talking about the cryptic genes in ΦX174. When conserved genes among the Microviridae family were erased (resulting in phage kleenX174), plaque size was reduced and therefore phage fitness was reduced, confirmed by creating chimeric genomes. This reduction in fitness was shown to be due to a nucleotide mutation in the ‘H protein’. Reverting the single nucleotide mutation back to wild type allowed the doubling of protein H production.
• Coming soon(ish), Paul and his team have some very exciting studies up next. One that particularly interested the audience was the creation of a Plaque Quantification Tool by Master's Student Ellina Trofimova – stay tuned!

Phage Directory is on YouTube!

Subscribe to Phage Directory's YouTube channel to keep up to date with future PHAVES recordings!

Sign up for PHAVES!

Register for upcoming PHAVES seminars — not only do we host speakers, interviews and AMAs, but we always host breakout rooms after the talks to encourage casual socializing/networking among the phage community!