Molecular Aspects and Comparative Genomics of Bacteriophage Endolysins

Abstract

Phages are recognized as the most abundant and diverse entities on the planet. Their diversity is determined predominantly by their dynamic adaptation capacities when confronted with different selective pressures in an endless cycle of coevolution with a widespread group of bacterial hosts. At the end of the infection cycle, progeny virions are confronted with a rigid cell wall that hinders their release into the environment and the opportunity to start a new infection cycle. Consequently, phages encode hydrolytic enzymes, called endolysins, to digest the peptidoglycan. In this work, we bring to light all phage endolysins found in completely sequenced double-stranded nucleic acid phage genomes and uncover clues that explain the phage-endolysin-host ecology that led phages to recruit unique and specialized endolysins.

DUF3380 Domain from a Salmonella Phage Endolysin Shows Potent N -Acetylmuramidase Activity

“…This modular structure is a common feature in endolysins with a Gram-positive background (7) but remains rare in endolysins with a Gram-negative background, which are mostly globular (22). Interestingly, the PG_binding_1 is also almost always restricted to Gram-positiverelated endolysins (8), although there are a few exceptions (Salmonella phage PVP-SE1; Pseudomonas phages phiKZ, EL, 201phi21, and OBP; and phages infecting Burkholderia and Erwinia) (21,23,33). The DUF3380 domain has only been predicted in endolysins from phages infecting Burkholderia, Pseudomonas, and Erwinia (33), and it is classified as a pfam domain of unknown function.…”

“…In general, most of the endolysins from phages infecting Gram-positive bacteria have a modular structure consisting of one or two N-terminal enzymatic active domains (EADs) and a C-terminal cell wall binding domain (CBD) separated by a short linker (7). In contrast, the vast majority of endolysins from phages infecting Gram-negative bacteria have a globular organization containing only an EAD, although a number of modular endolysins with different orientations of EADs and CBDs have also been described (4,8). The CBDs are responsible for the recognition of the substrate and the high-affinity binding of these enzymes to the bacterial cell wall (9), whereas the EADs are responsible for the catalytic activity, i.e., the cleavage of specific bonds within the PG.…”

Antimicrobial bacteriophage-derived proteins and therapeutic applications

“…19 (For an overview of endolysin types and activities, see refs.) 10,11 Endolysin derived from phages that infect Gram-positive hosts typically have a modular domain structure composed of Nterminal enzymatically active domain (EAD), and a C-terminal cell wall binding domain (CBD) connected by a short linker region (Fig. 3).…”

“…4 Concurrent to phage therapies, there have been efforts to develop antibacterial agents from the bacteriostatic and bacteriolytic proteins encoded by phages. 10,11 To date, the most notable are the phage-encoded peptidoglycan hydrolases (PGH), called endolysins. Endolysins are in part responsible for releasing newly formed viral particles by degrading peptidoglycan, which destabilizes the cell wall and causes the host cell to burst.…”

Bacteriophages and Their Derivatives as Biotherapeutic Agents in Disease Prevention and Treatment

“…Lysins are classified into five different groups depending on their cleavage site within the peptidoglycan. These are (1) N-acetyl--D-muramidase (lysozymes); (2) lytic transglycosylase; (3) N-acetyl--D-glucosaminidases (glycosidases), which hydrolyse the -1-4 glycosidic bond in the sugar moiety of the cell wall; (4) N-acetylmuramoyl-L-alanine amidases, which cleave the amide bond connecting the sugar and peptide moieties of the bacterial cell wall, and (5) L-alanoyl-Dglutamate endopeptidases and interpeptide bridge-specific endopeptidases, which attack the peptide moiety of the cell wall peptidoglycan (Figure 8) [96,[100][101][102]. If purified and applied exogenously, endolysins are only effective against Gram-positive bacteria; the outer membrane of Gramnegatives prevents access of exogenous Gram-negative endolysins [103].…”