Diversity, specificity and molecular evolution of the lytic arsenal of Pseudomonas phages: in silico perspective

Abstract

Summary Bacteriophages encode an arsenal of proteins to lyse bacteria by breaking their surface structures, constituting a promising alternative to antibiotics. However, the selection and bioengineering of endolysins and other phage lytic proteins need to be assisted by a previous knowledge of their molecular characteristics. In this study, all putative lytic proteins encoded in Pseudomonas phages were in silico examined to describe their diversity, host association and molecular evolution. A total of 491 proteins were identified among 223 phages, including endolysins, holins, pinholins, spanins, lipases and peptidases. Protein families and combination of functional domains were characteristic of phages belonging to the same genus, and these tended to infect a single host species. Clustering and phylogenetic analysis showed a protein grouping associated with bacterial host, and some functional domains being specific. Interestingly, most putative lytic proteins from phages infecting P. fluorescens and P. putida had negative net charges, opposed to most endolysins. Phage lifestyle also had an impact on protein variability, with transglycosylases, glucosaminidases, holins and spanins from lysogenic phages clustering into monophyletic nodes, suggesting the effect of a different selection pressure as a result of the co‐option of a new function in the lysogenized bacteria.

Genomic Characterisation of UFJF_PfDIW6: A Novel Lytic Pseudomonas fluorescens-Phage with Potential for Biocontrol in the Dairy Industry

“…The holin belongs to the bacteriophage holin family, superfamily II-like (Pfam accession PF16082; E-value: 2.1e −15 ). The PF16082 Pfam is commonly found in the genomes of Pseudomonas bacteriophages, as well as other holin-family proteins: PF05106, PF05449, PF10746, PF13272, PF16080, PF16082, PF16083, PF16085, and PF16931 [ 88 ].…”

“…The endolysin belongs to the phage lysozyme family (Glycoside hydrolase family 24; PF00959; E-value: 3.7e −4 ). Among the muramidase superfamily of endolysins, PF00959 is the most common Pfam domain in Pseudomonas phages endolysins [ 88 ]. In addition, the endolysin contains a signal peptide with a cleavage site at residue 26 (likelihood: 0.9005), and no transmembrane helices were found on its sequence.…”

The Future of Bacteriophage Therapy Will Promote Antimicrobial Susceptibility

“…If resistance is a form of evolutionary rescue, phage steering can decrease the probability of rescue. Rather than simply identifying phages that target bacteria of interest, in silico experiments and screening to invoke evolutionary pathways as well as direct treatment to specifically inhibit the evolution of resistance will bring a more directed approach to phage therapy ( 82 , 83 ). Phage steering with antimicrobials has been investigated in only a few host-phage combinations ( 46 , 63 , 65 ).…”

In silico analysis of diversity, specificity and molecular evolution of Stenotrophomonas phages

“…The co-occurrence of lytic proteins in the phage was found with Pearson correlation analysis using SPSS software (Frey, 2017). Also, the hypothetical evolutionary models for proteins of lytic arsenals were made into cladograms according to each family and the binary data containing the presence or absence of proteins in the phage genome (Valero-Rello, 2019).…”

“…Previously, in silico analyses have been carried out in Pseudomonas phages to understand the molecular nature of the lytic proteins to allow better usage of phages in association with antibiotics (Ryan et al ., 2009; Geredew Kifelew et al ., 2019; Valero‐Rello, 2019; Lauman and Dennis, 2021). The larger scope is to study host specificity at an intergenera level to develop phage treatment further and make it broad spectrum rather than host‐specific.…”