The RNA–RNA interactome between a phage and its satellite virus reveals a small RNA that differentially regulates gene expression across both genomes

Abstract

Satellite viruses are present across all domains of life, defined as subviral parasites that require infection by another virus for satellite progeny production. Phage satellites exhibit various regulatory mechanisms to manipulate phage gene expression to the benefit of the satellite, redirecting resources from the phage to the satellite, and often inhibiting phage progeny production. While small RNAs (sRNAs) are well documented as regulators of prokaryotic gene expression, they have not been shown to play a regulatory role in satellite‐phage conflicts. Vibrio cholerae encodes the phage inducible chromosomal island‐like element (PLE), a phage satellite, to defend itself against the lytic phage ICP1. Here, we use Hi‐GRIL‐seq to identify a complex RNA–RNA interactome between PLE and ICP1. Both inter‐ and intragenome RNA interactions were detected, headlined by the PLE sRNA, SviR. SviR is involved in regulating both PLE and ICP1 gene expression uniquely, decreasing ICP1 target translation and affecting PLE transcripts. The striking conservation of SviR across all known PLEs suggests the sRNA is deeply rooted in the PLE‐ICP1 conflict and implicates sRNAs as unidentified regulators of gene expression in phage–satellite interactions.

Nucleoid-associated proteins shape the global protein occupancy and transcriptional landscape of a clinical isolate ofVibrio cholerae

“…In the absence of H-NS, the later ORFs in PLE become de-repressed as evidenced by the observed substantial increase in RNA polymerase occupancy coinciding with the SviR promoter (Figure 3E, Supplementary Figure 5D). This is consistent with SviR expression being below the limit of detection in the absence of ICP1 infection [72] and the absence of H-NS allowing for transcription from the SviR promoter and RNA polymerase occupancy extending into downstream ORFs.…”

Nuclease genes occupy boundaries of genetic exchange between bacteriophages

“…To determine the splicing of ICP1’s interrupted TMP gene forms a full-length TMP gene, we analyzed previous RNA sequencing data generated during ICP1 infection (24, 50) with the NCBI Magic-BLAST tool, which is designed for detecting candidate intronic sequences from RNA sequencing data sets (28). From this analysis, we detected the splicing of the multiple ICP1 transcripts (Figure 3).…”

“…Previously, it was recognized that the DNA binding domains of ICP1 T5orf172 HEGs have homology to CapR (55), a transcriptional repressor of ICP1’s capsid expression encoded by phage-inducible chromosomal island-like elements (PLEs). PLEs are sub-viral parasites that exploit the ICP1 life cycle for their own mobilization (21–24, 26, 50, 55–58), inhibiting ICP1 progeny formation. This antagonism is frequently met with counter-adaptation by the phage (10, 18, 20, 59), providing a model system for the study of subcellular molecular co-evolution.…”

Nuclease genes occupy boundaries of genetic exchange between bacteriophages

“…To determine whether the splicing of ICP1’s interrupted TMP gene forms a full-length TMP gene, we analyzed previous RNA sequencing data generated during ICP1 infection ( 27 , 54 ) with the NCBI Magic-BLAST tool, which is designed for detecting candidate intronic sequences from RNA sequencing data sets ( 31 ). From this analysis, we detected the splicing of the multiple ICP1 transcripts (Figure 3 ).…”

“…Previously, it was recognized that the DNA binding domains of ICP1 T5orf172 HEGs have homology to CapR ( 59 ), a transcriptional repressor of ICP1’s capsid expression encoded by phage-inducible chromosomal island-like elements (PLEs). PLEs are sub-viral parasites that exploit the ICP1 life cycle for their own mobilization ( 24–27 , 29 , 54 , 59–62 ), inhibiting ICP1 progeny formation. This antagonism is frequently met with counter-adaptation by the phage ( 13 , 21 , 23 , 63 ), providing a model system for the study of subcellular molecular co-evolution.…”