Accommodation of Helical Imperfections in Rhodobacter sphaeroides Argonaute Ternary Complexes with Guide RNA and Target DNA

• Main Authors: Yiwei Liu, Daria Esyunina, Ivan Olovnikov, Marianna Teplova, Andrey Kulbachinskiy, Alexei A. Aravin, Dinshaw J. Patel
• Format: Article
• Language: English
• Published: Elsevier 2018-07-01
• Series: Cell Reports
• Online Access: http://www.sciencedirect.com/science/article/pii/S2211124718309161

Summary: Prokaryotic Argonaute (Ago) proteins were recently shown to target foreign genetic elements, thus making them a perfect model for studies of interference mechanisms. Here, we study interactions of Rhodobacter sphaeroides Ago (RsAgo) with guide RNA (gRNA) and fully complementary or imperfect target DNA (tDNA) using biochemical and structural approaches. We show that RsAgo can specifically recognize both the first nucleotide in gRNA and complementary nucleotide in tDNA, and both interactions contribute to nucleic acid binding. Non-canonical pairs and bulges on the target strand can be accommodated by RsAgo with minimal perturbation of the duplex but significantly reduce RsAgo affinity to tDNA. Surprisingly, mismatches between gRNA and tDNA induce dissociation of the guide-target duplex from RsAgo. Our results reveal plasticity in the ability of Ago proteins to accommodate helical imperfections, show how this might affect the efficiency of RNA silencing, and suggest a potential mechanism for guide release and Ago recycling. : Prokaryotic Argonaute proteins (pAgos) target foreign genetic elements. Liu et al. structurally and functionally characterize interactions of pAgo with guide RNA and fully complementary or imperfectly targeted DNA, reveal plasticity in the ability of Ago proteins to accommodate helical imperfections, and suggest a potential mechanism for guide release. Keywords: Rhodobacter sphaeroides Argonaute, RsAgo, guide RNA, target DNA, RNA-DNA heteroduplex, non-canonical base pairs and bulges