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Published September 12, 2013 | Supplemental Material + Accepted Version
Journal Article Open

Bacterial Argonaute Samples the Transcriptome to Identify Foreign DNA

Abstract

Eukaryotic Argonautes bind small RNAs and use them as guides to find complementary RNA targets and induce gene silencing. Though homologs of eukaryotic Argonautes are present in many bacteria and archaea, their small RNA partners and functions are unknown. We found that the Argonaute of Rhodobacter sphaeroides (RsAgo) associates with 15–19 nt RNAs that correspond to the majority of transcripts. RsAgo also binds single-stranded 22–24 nt DNA molecules that are complementary to the small RNAs and enriched in sequences derived from exogenous plasmids as well as genome-encoded foreign nucleic acids such as transposons and phage genes. Expression of RsAgo in the heterologous E. coli system leads to formation of plasmid-derived small RNA and DNA and plasmid degradation. In a R. sphaeroides mutant lacking RsAgo, expression of plasmid-encoded genes is elevated. Our results indicate that RNAi-related processes found in eukaryotes are also conserved in bacteria and target foreign nucleic acids.

Additional Information

© 2013 Elsevier Inc. Received: July 18, 2013; Revised: August 8, 2013; Accepted: August 8, 2013; Published: September 12, 2013. We thank Katalin Fejes Tóth and members of the Aravin lab for helpful discussion and comments on the manuscript. We thank Chia-Hung Wu, Shannon Park, and Gargi Kulkarni from Dianne Newman's lab for guidance with bacterial experiments and Konstantin Piatkov for helpful suggestions. We thank Timothy Donohue (University of Wisconsin-Madison), Shulin Chen (WSU), Rebecca Parales (UC Davis), and Carlos Ríos-Velázquez (UPR-Mayagüez) for provided reagents and bacterial strains. We are grateful to Todd Lowe (UCSC) for providing access to the genome browser. We thank Sailakshmi Subramanian (Mount Sinai) and Georgi Marinov and Sergei Manakov (Caltech) for help with bioinformatic and statistical analysis, and Igor Antoshechkin (Caltech) for help with RNA sequencing. We thank Gregory Donaldson and Vishnu Manoranjan for assistance with experiments. I.O. is a Center for Environmental Microbiology Interactions (CEMI) fellow at Caltech. This work was supported by grants from the National Institutes of Health (R01 GM097363, R00 HD057233 and DP2 OD007371A) and the Searle Scholar Award (to A.A.A.). D.K.N. is an Investigator of the Howard Hughes Medical Institute. RNA-seq, small RNA, and small DNA data were deposited in the Gene Expression Omnibus database under accession number GSE49865.

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August 19, 2023
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