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Bacterial Argonaute Samples the Transcriptome to Identify Foreign DNA

Olovnikov, Ivan and Chan, Ken and Sachidanandam, Ravi and Newman, Diane K. and Aravin, Alexei A. (2013) Bacterial Argonaute Samples the Transcriptome to Identify Foreign DNA. Molecular Cell, 51 (5). pp. 594-605. ISSN 1097-2765. PMCID PMC3809076. http://resolver.caltech.edu/CaltechAUTHORS:20140220-100231898

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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.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1016/j.molcel.2013.08.014DOIArticle
http://www.sciencedirect.com/science/article/pii/S109727651300587XPublisherArticle
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3809076PubMed CentralArticle
ORCID:
AuthorORCID
Newman, Diane K.0000-0003-1647-1918
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.
Group:Caltech Center for Environmental Microbial Interactions (CEMI)
Funders:
Funding AgencyGrant Number
NIHR01 GM097363
NIHR00 HD057233
NIHDP2 OD007371A
Searle Scholar AwardUNSPECIFIED
Caltech Center for Environmental Microbial Interactions (CEMI)UNSPECIFIED
PubMed Central ID:PMC3809076
Record Number:CaltechAUTHORS:20140220-100231898
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:20140220-100231898
Official Citation:Olovnikov, I., Chan, K., Sachidanandam, R., Newman, Dianne K., & Aravin, Alexei A. (2013). Bacterial Argonaute Samples the Transcriptome to Identify Foreign DNA. Molecular Cell, 51(5), 594-605. doi: http://dx.doi.org/10.1016/j.molcel.2013.08.014
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:43887
Collection:CaltechAUTHORS
Deposited By: Jason Perez
Deposited On:20 Feb 2014 23:24
Last Modified:26 Oct 2017 18:14

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