Bacterial Argonaute Sets Sail

RESEARCH HIGHLIGHTS NPG

BACTERIAL PHYSIOLOGY Bacterial argonaute sets sail

In eukaryotes, argonaute proteins RNAs (diRNAs)) highlighted a strong To investigate the ability of the have important roles in small RNA- bias towards RNAs that had uridine argonaute protein to recognize for- mediated gene silencing. In a recent at the first position - a feature that eign nucleic acids, the authors used issue of Molecular Cell, Alexei Aravin is also present in many of the small Escherichia coli as a heterologous and colleagues demonstrate a role RNAs bound by eukaryotic argonaute host and found that expression of for a bacterial argonaute protein in proteins. The authors found that R. sphaeroides argonaute reduced the silencing foreign nucleic acids. the diRNAs mapped to the majority yield of the expression plasmid and Argonaute proteins have been of the sense transcripts from the resulted in the degradation of plas- identified in a range of bacteria and R. sphaeroides chromosomes and mid DNA. Comparative analysis of archaea. Although several crystallo endogenous plasmids, in addition the transcriptomes of wild-type and graphic structures have been made to showing a strong bias towards the argonaute-deficient R. sphaeroides available, and there has been a argonaute expression plasmid. There showed no difference in overall preliminary characterization of was no evidence of a preference for gene expression; however, when a the substrate-binding properties of a particular primary or secondary plasmid that expressed luciferase some bacterial argonaute proteins, structure in the RNA precursor. and LacI was introduced into the few experimental insights into their This suggests that diRNAs are either R. sphaeroides argonaute-deficient in vivo biological functions have been directly derived from mRNAs or are strain, there was a twofold increase gained thus far. derived from the products of mRNA in the levels of the luciferase and The authors were interested in degradation. LacI transcripts, which suggests that the nucleic acid-binding properties A similar in-depth analysis of R. sphaeroides argonaute can repress of the argonaute protein from the R. sphaeroides argonaute-bound gene expression from an exogenous Rhodobacter sphaeroides and began 22–24 nucleotide small DNA fraction plasmid. by expressing and purifying the pro- (which the authors refer to as RNA- Clearly, there is a long way to go R. sphaeroides tein, before characterizing the bound interacting DNAs (riDNAs)) was to refine the details of the molecular nucleic acids. Two distinct fractions then carried out. The riDNAs were mechanisms involved, but this study argonaute can of bound nucleic acids were detected: complementary to the diRNAs and, provides the first experimental evi- repress gene a fraction of small RNAs, which were similarly to the diRNAs, mapped to dence to support the hypothesis that expression mostly 15–19 nucleotides in length, the R. sphaeroides chromosomes and bacterial argonaute proteins target and a fraction of small DNAs, which endogenous plasmids, although they foreign nucleic acids. from an were mostly 22–24 nucleotides in showed a stronger bias towards the Sheilagh Molloy exogenous length. argonaute expression plasmid than plasmid Cloning and sequencing of the the diRNAs. Further analysis of the ORIGINAL RESEARCH PAPER Olovnikov, I. et al. argonaute-bound RNAs (which the riDNAs showed enrichment for multi Bacterial argonaute samples the transcriptome to identify foreign DNA. Mol. Cell 51, 594–605 (2013) authors refer to as DNA-interacting copy transposon and phage genes.

NATURE REVIEWS | MICROBIOLOGY VOLUME 11 | NOVEMBER 2013