Abstract
Bacteriophages (phages) are viruses that infect bacteria. They are the most abundant biological entity on Earth (current estimates suggest there to be perhaps 1031 particles) and are found nearly everywhere. Temperate phages can integrate into the chromosome of their host, and prophages have been found in abundance in sequenced bacterial genomes. Prophages may modulate the virulence of their host in different ways, e.g., by the secretion of phage-encoded toxins or by mediating bacterial infectivity. Some 70% of Streptococcus pneumoniae (the pneumococcus)—a frequent cause of otitis media, pneumonia, bacteremia and meningitis—isolates harbor one or more prophages. In the present study, over 4000 S. pneumoniae genomes were examined for the presence of prophages, and nearly 90% were found to contain at least one prophage, either defective (47%) or present in full (43%). More than 7000 complete putative integrases, either of the tyrosine (6243) or serine (957) families, and 1210 full-sized endolysins (among them 1180 enzymes corresponding to 318 amino acid-long N-acetylmuramoyl-L-alanine amidases [LytAPPH]) were found. Based on their integration site, 26 different pneumococcal prophage groups were documented. Prophages coding for tRNAs, putative virulence factors and different methyltransferases were also detected. The members of one group of diverse prophages (PPH090) were found to integrate into the 3’ end of the host lytASpn gene encoding the major S. pneumoniae autolysin without disrupting it. The great similarity of the lytASpn and lytA PPH genes (85–92% identity) allowed them to recombine, via an apparent integrase-independent mechanism, to produce different DNA rearrangements within the pneumococcal chromosome. This study provides a complete dataset that can be used to further analyze pneumococcal prophages, their evolutionary relationships, and their role in the pathogenesis of pneumococcal disease.
Highlights
This model consists of two phases: (1) the circularization of the linear phage DNA molecule injected into the cell, and (2) the linear insertion of the phage DNA into the bacterial chromosome via the activity of a specific integrase (Int) that catalyzes the sitespecific recombination of the phage attachment site and bacterial attachment site
According to the data presented in this and previous studies, prophages are very common in S. pneumoniae: up to 90% of pneumococcal isolates may harbor temperate phages, nearly half of them appear to be defective and lack the genes involved in morphogenesis and lysis
These can be considered ‘defective’ pneumococcal prophage (PPH) that may be in a state of mutational decay (Casjens, 2003)
Summary
Bacteriophages (phages) are viruses that infect bacteria. They are the most abundant biological entities on Earth — current estimates suggest there to be close to 1031 phage particles (Mushegian, 2020) — and can be found nearly everywhere. Campbell (1962) was the first to propose a model for the integration of l prophage into the bacterial chromosome This model consists of two phases: (1) the circularization of the linear phage DNA molecule injected into the cell, and (2) the linear insertion of the phage DNA into the bacterial chromosome via the activity of a specific integrase (Int) that catalyzes the sitespecific recombination of the phage attachment site (attP) and bacterial attachment site (attB). These two sequences generally share a short stretch of identical bases (the core sequence) where this site-specific recombination occurs. Under certain circumstances (prophage induction), the prophage becomes excised from the bacterial chromosome and viral replication begins via the lytic cycle
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