Revisiting the host adhesion determinants of Streptococcus thermophilus siphophages

Abstract

Available 3D structures of bacteriophage modules combined with predictive bioinformatic algorithms enabled the identification of adhesion modules in 57 siphophages infecting Streptococcus thermophilus (St). We identified several carbohydrate-binding modules (CBMs) in so-called evolved distal tail (Dit) and tail-associated lysozyme (Tal) proteins of St phage baseplates. We examined the open reading frame (ORF) downstream of the Tal-encoding ORF and uncovered the presence of a putative p2-like receptor-binding protein (RBP). A 21 A resolution electron microscopy structure of the baseplate of cos-phage STP1 revealed the presence of six elongated electron densities, surrounding the core of the baseplate, that harbour the p2-like RBPs at their tip. To verify the functionality of these modules, we expressed GFP-or mCherry-coupled Tal and putative RBP CBMs and observed by fluorescence microscopy that both modules bind to their corresponding St host, the putative RBP CBM with higher affinity than the Tal-associated one. The large number of CBM functional domains in St phages suggests that they play a contributory role in the infection process, a feature that we previously described in lactococcal phages and beyond, possibly representing a universal feature of the siphophage host-recognition apparatus.

Characterization of the First Virulent Phage Infecting Oenococcus oeni, the Queen of the Cellars

“…As we failed to identify any other CBM in the phage using HHpred, it is very likely that the tail extension analyzed here harbors the receptor binding modules and constitutes therefore the bona fide RBP. This is in contrast with the reports of the simultaneous presence of a Tal extension carrying CBMs and a RBP in Moineauvirus and Brussowvirus S. thermophilus phages ( Lavelle et al, 2020 ). The fact that our current data are reflecting some diverging structure of the phage tail tip between Vinitor and other phages of LAB is not so surprising and is probably linked to the complex and specific outer structures of their bacterial hosts.…”

Conserved and Diverse Traits of Adhesion Devices from Siphoviridae Recognizing Proteinaceous or Saccharidic Receptors

“…It is found in closed or open conformations depending upon the state of the baseplate (see Section 4). Tals from most phages, however, are longer than~400 residues, and in some cases reaching up to 2000 residues or more [28]. HHpred [37] analysis of these Tals reveals that they possess an N-terminal domain resembling the Tal domains mentioned above, for which the structures have been determined, followed by an extension exhibiting large structural and functional diversity.…”

“…This IC complex is then completed by the RBP and other baseplate proteins, if present, as well as with the MTPs and the tail terminator, the protein that blocks the tail extension, resulting in the complete tail that is ready to attach to the capsid connector [20,22]. [7], T5 [9], SPP1 [9], c2 [23], p2 [24], 1358 [25], TP901-1 [21,26], Tuc2009 [27], PSA [13], STP1 [28], 80α [15]. Tape measure proteins (TMPs) are color-coded grey; distal tail proteins (Dits) are color-coded red; tail-associated lysozymes (Tals) are color-coded dark green (Nt-structural domain), light green (Tal extension), light blue for Tal extension tip bearing a receptor-binding domain; receptor-binding proteins (RBPs) are color-coded light blue; ancillary proteins and tail fibers are color-coded dark blue.…”

“…Structure prediction of phage 80α Tal C-terminus suggests that it may also possess a peptidoglycan cleavage activity [15]. In some streptococcal phages as DT1 [41] or STP1 [28], Tals carry one or several carbohydrate-binding domains, capable of binding the cell wall surface saccharidic receptors. However, many Tal extensions are not annotated functionally.…”

“…Dits can harbor one to two carbohydrate-binding modules (CBMs) inserted in the loops of their peripheral galectin domains (Figure 2c). These functionalized Dits, termed "evolved Dits" [44], have been documented in Lactobacillus phages [44,45], lactococcal phages [46,47], streptococcal phages [28], and beyond [46]. Of note, these CBMs are often observed to share the BppA CBM fold [46].…”