Bacteriophage-encoded depolymerases: their diversity and biotechnological applications

Abstract

Bacteriophages (phages), natural enemies of bacteria, can encode enzymes able to degrade polymeric substances. These substances can be found in the bacterial cell surface, such as polysaccharides, or are produced by bacteria when they are living in biofilm communities, the most common bacterial lifestyle. Consequently, phages with depolymerase activity have a facilitated access to the host receptors, by degrading the capsular polysaccharides, and are believed to have a better performance against bacterial biofilms, since the degradation of extracellular polymeric substances by depolymerases might facilitate the access of phages to the cells within different biofilm layers. Since the diversity of phage depolymerases is not yet fully explored, this is the first review gathering information about all the depolymerases encoded by fully sequenced phages. Overall, in this study, 160 putative depolymerases, including sialidases, levanases, xylosidases, dextranases, hyaluronidases, peptidases as well as pectate/pectin lyases, were found in 143 phages (43 Myoviridae, 47 Siphoviridae, 37 Podoviridae, and 16 unclassified) infecting 24 genera of bacteria. We further provide information about the main applications of phage depolymerases, which can comprise areas as diverse as medical, chemical, or food-processing industry.

Bacteriophage-encoded virion-associated enzymes to overcome the carbohydrate barriers during the infection process

“…The majority of hydrolases belong to the group of O-glycosyl hydrolases (EC 3.2.1), which use a water molecule to cleave specifically the O-glycosidic bonds of the polysaccharide. This group comprises sialidases, rhamnosidases, levanases, xylanases, and dextranases (Davies and Henrissat 1995; Pires et al 2016). Polysaccharide depolymerases for which experimental data are available are mainly derived from phages propagating on the most common human pathogens (Table 1).…”

“…A levanase catalyzes hydrolysis of the β-2,6-bond between fructose monomers in levan, which is present in Bacillus biofilms and has been identified in Bacillus phage SP10. A xylanase responsible for hydrolysis of the β-1,4 bonds within xylan has been identified in the Caulobacter phage Cr30, while a dextranase cleaving the α-1,6-linkages between glucose units in dextran is predicted in Lactobacillus phage ΦPYB5 (Pires et al 2016). Some virion-associated depolymerases do not depolymerize polysaccharides but cleave polypeptides (EC 3.4) or lipids (EC 3.1), responding to the different nature of some bacterial capsules.…”

“…Some reviews dealing with these phage-encoded, virion-associated enzymes have been published recently, particularly focusing on general characteristics and biomedical applications (Drulis-Kawa et al 2012, 2015; Yan et al 2014) or on virion-associated peptidoglycan hydrolases (VAPGHs) (Rodríguez-Rubio et al 2013a). Pires et al (2016) recently provided an overview of 160 putative depolymerases in 143 phages infecting 24 genera of bacteria based on an extensive in silico analysis. Here, we present a summary of experimentally confirmed polysaccharide depolymerases and virion-associated lysins (VALs) and focus on the main characteristics of the corresponding genes, their protein structure, their location within the virion particle, their mode of action and specificity, evolutionary aspects, methods for activity determination, and potential applications.…”

Emergence of a Competence-Reducing Filamentous Phage from the Genome of Acinetobacter baylyi ADP1

“…Knockout of pgi is also known to cause ADP1 cells to aggregate (15). Changes to the cell surface associated with this mutation, possibly related to the production of polysaccharides that mask the phage receptor (45,46) or that decrease the surface area accessible for phage adsorption, may lead to this partial resistance phenotype.…”

La phagothérapie

“…Une autre propriété remarquable de ces virus réside dans leur capacité à hydrolyser les polysaccharides bactériens qui composent les biofilms 4 , ou les exopolysaccharides de surface (capsules) produits par certaines bactéries. Ces enzymes (appelées dépoly-mérases) sont essentiellement portées par les fibres de queue de certains phages [14], leur conférant ainsi un avantage spécifique comparé aux antibiotiques, dont on connaît les limites en matière de pénétration dans les biofilms.…”