Bacteriophage characterization provides platform for rational design

(Press-News.org) From medicine to agriculture and aquaculture, bacteriophages are poised to have a huge global impact. As viruses which target only bacterial cells, they hold promise as an alternative to antibiotics, overcoming increasing issues around antibiotic resistance. However, the size, complexity and growth conditions of phages make them difficult to study, limiting progress in the field. Now in Science Advances, researchers from the Okinawa Institute of Science and Technology (OIST) and University of Otago describe the bacteriophage Bas63 in unprecedented detail, supporting new mechanistic understanding into how these viruses function.

Co-author Professor Matthias Wolf, head of the Molecular Cryo-Electron Microscopy Unit at OIST, says, “Very few phages have been described in such a level of molecular detail. By providing new structural insights and biological understanding, we can enable rational phage design and transform how diseases are treated.”

The complexity of bacteriophages

Bacteriophages are among the most abundant biological entities on Earth, first discovered in the 1910s. Early on, their potential to target bacterial infections was recognized. However, to this day the field of phage therapy remains largely underdeveloped. This is due to the discovery and development of antibiotics, which are far simpler to manufacture and administer than phages.

Now, with increasing challenges around antibiotic resistance, a new wave of phage research is underway. But to fuel this innovation, quality data is needed. Therefore, the researchers selected Bas63 to characterize from the BASEL collection which provides genomic and phenotypic data on over 100 bacteriophages known to infect E. coli.

"Bas63 has one of the most unique genomes and structures of its sub-family, based on simple low-resolution microscopy. This made it a prime target for high-resolution structural studies,” notes co-author Professor Mihnea Bostina of the University of Otago and visiting scholar at OIST.

Complete structural mapping

Using cryogenic electron microscopy (cryo-EM), they mapped the full structure of Bas63 in high resolution, applying a unique panning microscopy technique which ‘walks’ down the structure and shifts the focus of the reconstruction at each step. By combining amino acid sequence information with their electron microscopy data, they were able to resolve the full 3D structure of the bacteriophage, defining all the important structural proteins of Bas63 in minute detail. Amongst their many findings, they describe unique decoration proteins on the main body of the capsid, and a rare whisker and collar structure connecting the phage head to its tail.

Through comparison to proteins of other bacteriophages within the sub-family, they also identified target regions for phage design and engineering efforts. Prof. Bostina explains, “Significant sequence differences were found in the tail fiber proteins of the bacteriophages. This may indicate that they play a specific role in bacterial host recognition, so could be important phage engineering targets when designing for specificity.”

New phage frontiers: from biotechnology to art

The researchers hope this work will inspire future bacteriophages research in a variety of fields. “Outside of medicine, bacterial pathogens can affect crops and livestock. Industries such as water treatment, food processing and energy production are also often challenged by bacterial biofilms,” highlights Prof. Wolf. “Beyond scientific applications, detailed 3D information can be useful in design and animation, so artists, developers and educators may find creative inspiration from our data”.

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