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Updated: May 7, 2026
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PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins
Published on: July 2, 2010
Bacterial argonaute samples the transcriptome to identify foreign DNA.
Ivan Olovnikov1, Ken Chan, Ravi Sachidanandam
1Division of Biology, California Institute of Technology, 147-75, 1200E California Boulevard, Pasadena, CA 91125, USA; Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov Square 2, Moscow 123182, Russia.
Molecular Cell
|September 17, 2013
Summary
Bacterial Argonaute proteins bind small RNAs and DNA to target foreign nucleic acids, revealing conserved RNA interference-related processes in bacteria. This bacterial Argonaute system degrades foreign DNA and RNA, impacting gene expression.
Area of Science:
- Microbiology
- Molecular Biology
- Genetics
Background:
- Eukaryotic Argonaute proteins bind small RNAs to guide gene silencing.
- Bacterial and archaeal Argonaute homologs' functions and small RNA partners remain largely unknown.
- Investigating bacterial Argonaute function is crucial for understanding prokaryotic gene regulation and defense.
Purpose of the Study:
- To identify the small RNA partners and functions of the Argonaute protein from Rhodobacter sphaeroides (RsAgo).
- To determine if bacterial Argonaute proteins target foreign nucleic acids.
- To explore the conservation of RNA interference (RNAi)-related processes in bacteria.
Main Methods:
- Affinity purification of RsAgo and associated small RNAs and DNAs.
- Expression of RsAgo in a heterologous Escherichia coli system.
- Analysis of plasmid gene expression in wild-type and RsAgo-deficient Rhodobacter sphaeroides mutants.
Main Results:
- RsAgo associates with 15-19 nt small RNAs corresponding to most transcripts.
- RsAgo binds single-stranded 22-24 nt DNA molecules complementary to small RNAs, originating from plasmids and foreign genomic elements.
- RsAgo expression in E. coli induced small RNA/DNA formation and plasmid degradation; its absence in R. sphaeroides elevated plasmid gene expression.
Conclusions:
- Bacterial Argonaute proteins utilize small RNAs and DNA to target foreign nucleic acids.
- RNAi-related processes are conserved in bacteria and function to defend against foreign genetic elements.
- RsAgo plays a role in bacterial defense mechanisms against mobile genetic elements and plasmids.
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