Bacteriophage N4 large terminase: expression, purification and X-ray crystallographic analysis

WGS analysis of two Staphylococcus aureus bacteriophages from sewage in China provides insights into the genetic feature of highly efficient lytic phages

The study of bacteriophages is experiencing a resurgence with the increasing development of antimicrobial resistance in Staphylococcus aureus. Nonetheless, the genetic features of highly efficient lytic S. aureus phage remain to be explored. In this study, two lytic S. aureus phages, SapYZU11 and SapYZU15, were isolated from sewage samples from Yangzhou, China. The phage morphology, one-step growth, host spectrum and lytic activity of these phages were examined, and their whole-genome sequences were analysed and compared with 280 published genomes of staphylococcal phages. The structural organisation and genetic contents of SapYZU11 and SapYZU15 were investigated. The Podoviridae phage SapYZU11 and Herelleviridae phage SapYZU15 effectively lysed all of the 53 S. aureus strains isolated from various sources. However, SapYZU15 exhibited a shorter latent period, larger burst size and stronger bactericidal ability with an anti-bacterial rate of approximately 99.9999% for 24 h. Phylogenetic analysis revealed that Herelleviridae phages formed the most ancestral clades and the S. aureus Podoviridae phages were clustered in the staphylococcal Siphoviridae phage clade. Moreover, phages in different morphology families contain distinct types of genes associated with host cell lysis, DNA packaging and lysogeny. Notably, SapYZU15 harboured 13 DNA metabolism-related genes, 5 lysin genes, 1 holin gene and 1 DNA packaging gene. The data suggest that S. aureus Podoviridae and Siphoviridae phages originated from staphylococcal Herelleviridae phages, and the module exchange of S. aureus phages occurred in the same morphology family. Moreover, the extraordinary lytic capacity of SapYZU15 was likely due to the presence of specific genes associated with DNA replication, DNA packaging and the lytic cycle.

Whole-Genome Analysis Reveals That Bacteriophages Promote Environmental Adaptation of Staphylococcus aureus via Gene Exchange, Acquisition, and Loss

The study of bacteriophages is experiencing a resurgence owing to their antibacterial efficacy, lack of side effects, and low production cost. Nonetheless, the interactions between Staphylococcus aureus bacteriophages and their hosts remain unexplored. In this study, whole-genome sequences of 188 S. aureus bacteriophages—20 Podoviridae, 56 Herelleviridae, and 112 Siphoviridae—were obtained from the National Center for Biotechnology Information (NCBI, USA) genome database. A phylogenetic tree was constructed to estimate their genetic relatedness using single-nucleotide polymorphism analysis. Comparative analysis was performed to investigate the structural diversity and ortholog groups in the subdividing clusters. Mosaic structures and gene content were compared in relation to phylogeny. Phylogenetic analysis revealed that the bacteriophages could be distinguished into three lineages (I–III), including nine subdividing clusters and seven singletons. The subdividing clusters shared similar mosaic structures and core ortholog clusters, including the genes involved in bacteriophage morphogenesis and DNA packaging. Notably, several functional modules of bacteriophages 187 and 2368A shared more than 95% nucleotide sequence identity with prophages in the S. aureus strain RJ1267 and the Staphylococcus pseudintermedius strain SP_11306_4, whereas other modules exhibited little nucleotide sequence similarity. Moreover, the cluster phages shared similar types of holins, lysins, and DNA packaging genes and harbored diverse genes associated with DNA replication and virulence. The data suggested that the genetic diversity of S. aureus bacteriophages was likely due to gene replacement, acquisition, and loss among staphylococcal phages, which may have crossed species barriers. Moreover, frequent module exchanges likely occurred exclusively among the subdividing cluster phages. We hypothesize that during evolution, the S. aureus phages enhanced their DNA replication in host cells and the adaptive environment of their host.

The coevolution of large and small terminases of bacteriophages is a result of purifying selection leading to phenotypic stabilization

Genome packaging in many dsDNA phages requires a series of precisely coordinated actions of two phage-coded proteins, namely, large terminase (TerL) and small terminase (TerS) with DNA and ATP, and with each other. Despite the strict functional conservation, TerL and TerS homologs exhibit large sequence variations. We investigated the sequence variability across eight phage types and observed a coevolutionary framework wherein the genealogy of TerL homologs mirrored that of the corresponding TerS homologs. Furthermore, a high purifying selection observed (dN/dS«1) indicated strong structural constraints on both TerL and TerS, and identify coevolving residues in TerL and TerS of phage T4 and lambda. Using the highly coevolving (correlation coefficient of 0.99) TerL and TerS of phage N4, we show that their biochemical features are similar to the phylogenetically divergent phage λ terminases. We also demonstrate using the Surface Plasma Resonance (SPR) technique that phage N4 TerL transiently interacts with TerS.

Genomic characterization of four novel bacteriophages infecting the clinical pathogen Klebsiella pneumoniae

Bacteriophages are an invaluable source of novel genetic diversity. Sequencing of phage genomes can reveal new proteins with potential uses as biotechnological and medical tools, and help unravel the diversity of biological mechanisms employed by phages to take over the host during viral infection. Aiming to expand the available collection of phage genomes, we have isolated, sequenced, and assembled the genome sequences of four phages that infect the clinical pathogen Klebsiella pneumoniae: vB_KpnP_FBKp16, vB_KpnP_FBKp27, vB_KpnM_FBKp34, and Jumbo phage vB_KpnM_FBKp24. The four phages show very low (0–13%) identity to genomic phage sequences deposited in the GenBank database. Three of the four phages encode tRNAs and have a GC content very dissimilar to that of the host. Importantly, the genome sequences of the phages reveal potentially novel DNA packaging mechanisms as well as distinct clades of tubulin spindle and nucleus shell proteins that some phages use to compartmentalize viral replication. Overall, this study contributes to uncovering previously unknown virus diversity, and provides novel candidates for phage therapy applications against antibiotic-resistant K. pneumoniae infections.