Exploring Host-Binding Machineries of Mycobacteriophages with AlphaFold2

Christian Cambillau (1) , Adeline Goulet (2)

1 UCC - University College Cork
2 LISM - Laboratoire d'ingénierie des systèmes macromoléculaires

Although more than 12,000 bacteriophages infecting mycobacteria (mycobacteriophages) have been isolated so far, there is a knowledge gap on their structure-function relationships. Here, we have explored the architecture of host-binding machineries from seven representative mycobacteriophages of the Siphoviridae family infecting Mycobacterium smegmatis, Mycobacterium abscessus, and Mycobacterium tuberculosis, using AlphaFold2 (AF2). AF2 enables confident structural analyses of large and flexible biological assemblies resistant to experimental methods, thereby opening new avenues to shed light on phage structure and function. Our results highlight the modularity and structural diversity of siphophage host-binding machineries that recognize host-specific receptors at the onset of viral infection. Interestingly, the studied mycobacteriophages' host-binding machineries present unique features compared with those of phages infecting other Gram-positive actinobacteria. Although they all assemble the classical Dit (distal tail), Tal (tail-associated lysin), and receptor-binding proteins, five of them contain two potential additional adhesion proteins. Moreover, we have identified brush-like domains formed of multiple polyglycine helices which expose hydrophobic residues as potential receptor-binding domains. These polyglycine-rich domains, which have been observed in only five native proteins, may be a hallmark of mycobacteriophages' host-binding machineries, and they may be more common in nature than expected. Altogether, the unique composition of mycobacteriophages' host-binding machineries indicate they might have evolved to bind to the peculiar mycobacterial cell envelope, which is rich in polysaccharides and mycolic acids. This work provides a rational framework to efficiently produce recombinant proteins or protein domains and test their host-binding function and, hence, to shed light on molecular mechanisms used by mycobacteriophages to infect their host.

Mots clés: bacteriophage; Mycobacteria; AlphaFold2; host-binding machineries; carbohydrate-binding module; receptor-binding protein; polyglycine helices

Domaines: Virologie; Biologie structurale [q-bio.BM]

Christian Cambillau, Adeline Goulet. Exploring Host-Binding Machineries of Mycobacteriophages with AlphaFold2. Journal of Virology, 2023, 97 (3), pp.01793-22. ⟨10.1128/jvi.01793-22⟩. ⟨hal-04274513⟩