Reprogramming Bacteriophage Host Range through Structure-Guided Design of Chimeric Receptor Binding Proteins

• Published in: Cell reports (Cambridge) 2019-10, Vol.29 (5), p.1336-1350.e4
• Main Authors: Dunne, Matthew, Rupf, Beatrice, Tala, Marc, Qabrati, Xhem, Ernst, Patrick, Shen, Yang, Sumrall, Eric, Heeb, Laura, Plückthun, Andreas, Loessner, Martin J., Kilcher, Samuel
• Format: Article
• Language: English
• Subjects: bacteriophage; chimeric phage; directed evolution; host range; listeria; phage engineering; receptor binding protein; synthetic biology; tail spike; X-ray crystallography
• ISSN: 2211-1247; 2211-1247
• DOI: 10.1016/j.celrep.2019.09.062

Bacteriophages provide excellent tools for diagnostics, remediation, and targeted microbiome manipulation, yet isolating viruses with suitable host specificity remains challenging. Using Listeria phage PSA, we present a synthetic biology blueprint for host-range engineering through targeted modification of serovar-specific receptor binding proteins (RBPs). We identify Gp15 as the PSA RBP and construct a synthetic phage library featuring sequence-randomized RBPs, from which host range mutants are isolated and subsequently integrated into a synthetic, polyvalent phage with extended host range. To enable rational design of chimeric RBPs, we determine the crystal structure of the Gp15 receptor-binding carboxyl terminus at 1.7-Å resolution and employ bioinformatics to identify compatible, prophage-encoded RBPs targeting different Listeria serovars. Structure-guided design enables exchange of heterologous RBP head, neck, or shoulder domains to generate chimeric phages with predictable and extended host ranges. These strategies will facilitate the development of phage biologics based on standardized virus scaffolds with tunable host specificities. [Display omitted] •Adaptation of Listeria phage serovar specificity through targeted RBP variations•High-resolution crystal structure of a Listeria phage receptor binding protein•Structure-guided design of RBP chimeras yields phages with predictable host ranges•Synthetic RBPs extend phage binding specificity (from SV 4b to 4a, 4b, 4d, 5, 6b) Receptor binding proteins (RBPs) are key determinants of bacteriophage host range. Dunne et al. solve the RBP crystal structure of Listeria phage PSA and combine synthetic biology with structure-guided approaches to re-program RBP specificity. Using the temperate, narrow host range PSA scaffold, they construct virulent phages with extended and defined host specificities.