viruses Review Molecular Basis of Bacterial Host Interactions by Gram-Positive Targeting Bacteriophages Matthew Dunne * ID , Mario Hupfeld, Jochen Klumpp and Martin J. Loessner Institute of Food Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland; [email protected] (M.H.); [email protected] (J.K.); [email protected] (M.J.L.) * Correspondence: [email protected] Received: 2 July 2018; Accepted: 25 July 2018; Published: 28 July 2018 Abstract: The inherent ability of bacteriophages (phages) to infect specific bacterial hosts makes them ideal candidates to develop into antimicrobial agents for pathogen-specific remediation in food processing, biotechnology, and medicine (e.g., phage therapy). Conversely, phage contaminations of fermentation processes are a major concern to dairy and bioprocessing industries. The first stage of any successful phage infection is adsorption to a bacterial host cell, mediated by receptor-binding proteins (RBPs). As the first point of contact, the binding specificity of phage RBPs is the primary determinant of bacterial host range, and thus defines the remediative potential of a phage for a given bacterium. Co-evolution of RBPs and their bacterial receptors has forced endless adaptation cycles of phage-host interactions, which in turn has created a diverse array of phage adsorption mechanisms utilizing an assortment of RBPs. Over the last decade, these intricate mechanisms have been studied intensely using electron microscopy and X-ray crystallography, providing atomic-level details of this fundamental stage in the phage infection cycle. This review summarizes current knowledge surrounding the molecular basis of host interaction for various socioeconomically important Gram-positive targeting phage RBPs to their protein- and saccharide-based receptors. Special attention is paid to the abundant and best-characterized Siphoviridae family of tailed phages. Unravelling these complex phage-host dynamics is essential to harness the full potential of phage-based technologies, or for generating novel strategies to combat industrial phage contaminations. Keywords: gram-positive bacteria; bacteriophage; infection; receptor-binding proteins; phage technology; Listeria monocytogenes; Lactococcus lactis; Bacillus subtilis; Staphylococcus aureus 1. Introduction Bacteriophages (phages) are viruses that specifically infect bacteria. As the most abundant and ubiquitous biological entities on Earth, with an estimated global population of >1031 particles [1], phages play important roles in global ecology and bacterial pathogenicity [2,3]. The first stage of any successful phage infection is adsorption to a suitable host cell. Typically, this involves an initial, reversible, interaction with host cell receptors, before irreversible binding through tighter binding to the initial receptors or through interaction with secondary receptors [4]. Successful host adsorption is a prerequisite to cell wall degradation, penetration, and subsequent DNA transfer into the bacterial host. Receptor binding proteins (RBPs), usually located on the distal end of the phage tail apparatus, mediate binding to the host cell. These proteins of varying complexity and composition interact with a variety of bacterial host receptors, proteins, saccharides, and organelles [5,6] (Figure1). Over the last decade, X-ray crystallography and electron microscopy (EM) studies have illustrated a number of phage-host adsorption processes with extraordinary levels of atomic detail [7]. For instance, Taylor et al. used cryo-EM to determine the multifaceted E. coli phage T4 baseplate in pre- and post-host Viruses 2018, 10, 397; doi:10.3390/v10080397 www.mdpi.com/journal/viruses Viruses 2018, 10, 397 2 of 25 Viruses 2018, 10, x FOR PEER REVIEW 2 of 25 attachmentin pre- and states, post-host revealing attachment atomic states, resolution revealing details atomic of conformation resolution details changes of conformation to the baseplate changes prior to DNAto ejection the baseplate [8] that prior appear to DNA conserved ejection [8] in that other appear contractile conserved injection in other systems, contractile e.g., injection R-type systems, pyocins [9] and thee.g., bacterial R-type pyocins type VI [9] secretion and the systembacterial (T6SS) type VI [10 secretion]. Furthermore, system (T6SS)Hu et [10]. al. usedFurthermore, cryo-EM Hu to et reveal al. the phageused T4 tailcryo-EM tube penetrationto reveal the ofphage the bacterialT4 tail tube periplasm penetration that of induces the bacterial curvature periplasm of the that inner induces cytoplasm priorcurvature to DNA of ejection the inner [11 cytoplasm]. Bacillus prior subtilis to DNAphage ejection SPP1 [11]. [12 Bacillus–15], andsubtilisLactococcal phage SPP1phages [12–15], p2 and [16 ,17] Lactococcal phages p2 [16,17] and TP901-1 [18,19], among others [20,21] described in this review, have and TP901-1 [18,19], among others [20,21] described in this review, have become model systems for become model systems for understanding the adsorption processes of phages that target Gram- understandingpositive bacteria. the adsorption processes of phages that target Gram-positive bacteria. Figure 1. Host cell receptors of Gram-positive targeting phages. Surrounding the cytoplasmic Figure 1. Host cell receptors of Gram-positive targeting phages. Surrounding the cytoplasmic membrane is a complex arrangement of different biopolymers that are receptors for different phages: membranepeptidoglycan is a complex (PG) (described arrangement in Section of different 8), teichoic biopolymers acids (Sections that 9–12), are receptors polysaccharides for different such as phages: a peptidoglycanpellicle layer (PG) (Sections (described 13 and in 14), Section and 8protruding), teichoic organelles acids (Sections such as9– 12the), flagella polysaccharides (Section 15). such as a pellicleHighlighted layer are (Sections known host 13 cell and receptors 14), and for protruding four different organelles Caudovirales such phages as thedescribed flagella within (Section this 15). Highlightedreview: Siphoviridae are known L. host lactis cell phage receptors TP901-1 for [22] four and different B. subtilisCaudovirales phage PBS1phages [23], Podoviridae described S. aureus within this review:phageSiphoviridae ϕ66 [24], and L. lactisMyoviridaephage Listeria TP901-1 phage [22 A511] and [20].B. subtilis phage PBS1 [23], Podoviridae S. aureus phage φ66 [24], and Myoviridae Listeria phage A511 [20]. The natural ability of phages to infect (and kill) a certain bacterial host range has led to their exploitation over the past decades for the development of diagnostic tools and antibacterials for use inThe medicine natural [25,26], ability food of phagesproduction to infect[27–31], (and and biotechnology kill) a certain [32–34]. bacterial For hostexample, range phages has ledcan tobe their exploitationused to treat over Campylobacter the past decades [35] or for Salmonella the development [27] infections of diagnosticof chicken flocks, tools or and added antibacterials to feed to kill for use in medicineClostridium [25 ,and26], intestinal food production coliforms [ 27in –pigs31], [36]; and added biotechnology to ready-to-eat [32–34 foods]. For to example, prevent Salmonella phages can be used[37] to treat or ListeriaCampylobacter [38] contaminations;[35] or Salmonella or mixed[ 27with] infections various food of chickenproducts flocks, to act as or bio-preservatives added to feed to kill Clostridium[39–41].and Phages intestinal and recombinant coliforms in RBPs pigs [have36]; addedbeen engineered to ready-to-eat into affinity foods to molecules prevent Salmonellafor rapid [37] or Listeriabiosensor-based[38] contaminations; detection of orStaphylococcus mixed with aureus various [42,43], food Salmonella products [44,45], to act asCampylobacter bio-preservatives jejuni [35], [39 –41]. Phagesor Shigella and recombinant flexneri [46],RBPs or attached have beento magnetic engineered beads intofor rapid affinity immobilization, molecules for magnetic rapidbiosensor-based separation, detectionand detection of Staphylococcus of Salmonella aureus [30]. However,[42,43], virulentSalmonella phages[44 ,also45], presentCampylobacter significant jejuni challenges[35], to or anyShigella biotechnological process that is reliant on bacteria, e.g., recombinant therapeutics in E. coli [47], milk flexneri [46], or attached to magnetic beads for rapid immobilization, magnetic separation, and detection fermentation to produce cheese and yogurt [48], and many more. Phage infection of lactic acid of Salmonellabacteria (LAB)[30]. However,starter cultures virulent remains phages the biggest also present threat significantfor dairy fermentation, challenges tocausing any biotechnological inadequate processmilk that acidification, is reliant poor on bacteria, quality products, e.g., recombinant and significant therapeutics economic inlosses.E. coli Addressing[47], milk this fermentation problem to produceis a significant cheese and challenge yogurt due [48 ],to and the ubiquitous many more. presence Phage of infection LAB-infecting of lactic phages acid in bacteria the environment. (LAB) starter culturesLactococcus remains lactis the is biggest the most threat important for dairy bacterial fermentation, species for causing the production inadequate ofmilk cheese, acidification, and, poorconsequently, quality products, its phages and significanthave been economicintensively losses.studied Addressingworldwide, thismainly problem with the is aaim