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An Assay for Quantifying Protein-RNA Binding in Bacteria
Published on: June 12, 2019
The RNA-RNA interactome between a phage and its satellite virus reveals a small RNA that differentially regulates
Drew T Dunham1, Angus Angermeyer1, Kimberley D Seed1
1Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA.
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.
Insights
Phage satellites use small RNAs (sRNAs) to control viral conflicts. Researchers discovered a specific sRNA, SviR, that regulates gene expression in both the satellite and its target phage, ICP1.
Area of Science:
- Microbiology
- Virology
- Molecular Biology
Background:
- Satellite viruses are subviral parasites dependent on helper viruses for replication.
- Phage satellites employ regulatory strategies to manipulate host phage gene expression.
- The role of small RNAs (sRNAs) in satellite-phage interactions remains largely unexplored.
Purpose of the Study:
- To investigate the RNA-RNA interactome between the Vibrio cholerae phage satellite PLE and its target phage ICP1.
- To identify regulatory small RNAs involved in the PLE-ICP1 conflict.
- To elucidate the function of the identified sRNA in modulating gene expression.
Main Methods:
- High-throughput Genome-wide RNA Interactome capture followed by sequencing (Hi-GRIL-seq) was employed.
- RNA sequencing data was analyzed to identify RNA-RNA interactions within and between PLE and ICP1 genomes.
- Functional analysis of specific sRNAs was performed to assess their regulatory roles.
Main Results:
- A complex RNA-RNA interactome between PLE and ICP1 was identified, including both inter- and intragenomic interactions.
- A PLE-encoded small RNA, SviR, was identified as a key regulator in the interaction.
- SviR was shown to decrease ICP1 target translation and affect PLE transcripts, demonstrating dual regulatory control.
Conclusions:
- Small RNAs, exemplified by SviR, play a significant role in regulating gene expression during phage-satellite conflicts.
- The conserved nature of SviR suggests its fundamental importance in the PLE-ICP1 antagonistic relationship.
- This study implicates sRNAs as critical, previously unrecognized regulators in phage-satellite interactions.
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