Phage-encoded ribosomal protein S21 expression is linked to late-stage phage replication

Abstract

The ribosomal protein S21 (bS21) gene has been detected in diverse viruses with a large range of genome sizes, yet its in situ expression and potential significance have not been investigated. Here, we report five closely related clades of bacteriophages (phages) represented by 47 genomes (8 curated to completion and up to 331 kbp in length) that encode a bS21 gene. The bS21 gene is on the reverse strand within a conserved region that encodes the large terminase, major capsid protein, prohead protease, portal vertex proteins, and some hypothetical proteins. Based on CRISPR spacer targeting, the predominance of bacterial taxonomic affiliations of phage genes with those from Bacteroidetes, and the high sequence similarity of the phage bS21 genes and those from Bacteroidetes classes of Flavobacteriia, Cytophagia and Saprospiria, these phages are predicted to infect diverse Bacteroidetes species that inhabit a range of depths in freshwater lakes. Thus, bS21 phages have the potential to impact microbial community composition and carbon turnover in lake ecosystems. The transcriptionally active bS21-encoding phages were likely in the late stage of replication when collected, as core structural genes and bS21 were highly expressed. Thus, our analyses suggest that the phage bS21, which is involved in translation initiation, substitutes into the Bacteroidetes ribosomes and selects preferentially for phage transcripts during the late-stage replication when large-scale phage protein production is required for assembly of phage particles.

Variable impact of geochemical gradients on the functional potential of bacteria, archaea, and phages from the permanently stratified Lac Pavin

“…Approximately 7.7% of phage scaffolds were circularized and thus likely represent complete genome sequences (Table S9). We merged these newly-reported phage scaffolds with those from our previous studies of the same environment [26,27] and subjected the total set of ∼800 non-redundant phage scaffolds to a network analysis based on protein content.…”

“…Approximately 7.7% of phage scaffolds were circularized and thus likely represent complete genome sequences (Table S9). We merged these newly-reported phage scaffolds with those from our previous studies of the same environment [26,27] and subjected the total set of ~800 non-redundant phage scaffolds to a network analysis based on protein content. This analysis revealed that many phages from Lac Pavin fall into broad clusters with known phages from diverse environments, suggesting they are part of well-sampled clades defined by protein content ("mixed" clusters, Fig.…”

“…5a). Of particular interest were Lac Pavin phage scaffolds that clustered with megaphages from diverse environments [26], phages encoding the S21 ribosomal protein from freshwater environments [27], and phages from another large freshwater lake in Japan, Lake Biwa [28] (Fig. 5b).…”

“…Putative phage scaffolds were integrated with those published previously from a subset of Lac Pavin metagenomes [26,27], many of which were manually curated to completion. Distribution of the integrated set of phages was determined by stringent re-mapping of sequencing reads to the combined scaffold set as described above for bacterial and archaeal genomes.…”

A Ribosomal Protein Homolog Governs Gene Expression and Virulence in a Bacterial Pathogen

“…The idea that bS21 might modulate translation for a subset of mRNAs is further supported by the recent discovery that bS21 is encoded by thousands of sequenced bacteriophage genomes and is one of the most commonly encoded phage ribosomal proteins ( 52 , 53 ). Transcripts encoding bS21 have been detected in metatranscriptomic samples along with transcripts for late-stage replication proteins ( 54 ) and at least one phage-encoded bS21 can be incorporated into E. coli ribosomes ( 52 ). All of this raises the possibility that the incorporation of a viral bS21 into the host ribosome may co-opt the translation machinery in favor of viral proteins and replication.…”