Cambillau, C. | Search bioRxiv

bioRxiv2025

Isolation of phages infecting the zoonotic pathogen Streptococcus suis reveals novel structural and genomic characteristics

Bacteriophage research has experienced a renaissance in recent years, owing to their therapeutic potential and versatility in biotechnology, particularly in combating antibiotic resistant-bacteria along the farm-to-fork continuum. However, certain pathogens remain underexplored as targets for phage therapy, including the zoonotic pathogen Streptococcus suis which causes infections in pigs and humans. Despite global efforts, the genome of only one infective S. suis phage has been described. Here, we report the isolation of two phages that infect S. suis: Bonnie and Clyde. The phages infect 58% of 100 S. suis strains tested, including representatives of seven different serotypes and thirteen known sequence types from diverse geographical origins. Clyde suppressed bacterial growth in vitro within two multi-strain mixes designed to simulate a polyclonal S. suis infection. Both phages demonstrated stability across various temperatures and pH levels, highlighting their potential to withstand storage conditions and maintain viability in delivery formulations. Genome comparisons revealed that neither phage shares significant nucleotide identity with any cultivated phages in the NCBI database and thereby represent novel species belonging to two distinct novel genera. This study is the first to investigate the adhesion devices of S. suis infecting phages. Structure prediction and analysis of adhesion devices with AlphaFold2 revealed two distinct lineages of S. suis phages: Streptococcus thermophilus-like (Bonnie) and S. suis-like (Clyde). The structural similarities between the adhesion devices of Bonnie and S. thermophilus phages, despite the lack of nucleotide similarity and differing ecological niches, suggest a common ancestor or convergent evolution, highlighting evolutionary links between pathogenic and non-pathogenic streptococcal species. These findings provide valuable insights into the genetic and phenotypic characteristics of phages that can infect S. suis, providing new data for the therapeutic application of phages in a One Health context.

microbiology↗

bioRxiv2022

CbpD crystal structure adds intrigue to substrate-specificity motifs in chitin-active lytic polysaccharide monooxygenases

Pseudomonas aeruginosa secretes diverse proteins via its Type 2 Secretion System, including a 39 KDa Chitin-Binding Protein, CbpD. CbpD was recently shown to be a lytic polysaccharide monooxygenase active on chitin, and to contribute substantially to virulence. To-date no structure of this virulence factor has been reported. Its first two domains are homologous to those found in the crystal structure of Vibrio cholerae GbpA, while the third domain is homologous to the NMR structure of the Cellvibrio japonicus CjLPMO10A CBM73 domain. We report the 3.0 [A] resolution crystal structure of CbpD solved by molecular replacement, which required ab initio models of each CbpD domain generated by the artificial intelligence deep learning structure prediction algorithm RoseTTAFold. The structure of CbpD confirms previously postulated chitin-specific motifs in the AA10 domain while challenging the deterministic effects of other postulated substrate specificity motifs. Additionally, the structure of CbpD shows that post translational modifications occur on the chitin binding surface. Moreover, the structure raises interesting possibilities about how Type 2 Secretion System substrates may interact with the secretion machinery and demonstrates the utility of new artificial intelligence protein structure prediction algorithms in making challenging structural targets tractable.

microbiology↗