Argonaute bypasses cellular obstacles without hindrance during target search

• Published in: Nature communications Vol. 10; no. 1; pp. 4390 - 11
• Main Authors: Cui, Tao Ju, Klein, Misha, Hegge, Jorrit W, Chandradoss, Stanley D, van der Oost, John, Depken, Martin, Joo, Chirlmin
• Format: Journal Article
• Language: English
• Published: England Nature Publishing Group 26.09.2019; Nature Publishing Group UK; Nature Portfolio
• Subjects: Acids; Argonaute Proteins - chemistry; Argonaute Proteins - genetics; Argonaute Proteins - metabolism; Bacterial Proteins - chemistry; Bacterial Proteins - genetics; Bacterial Proteins - metabolism; Base Sequence; Bypasses; Clostridium butyricum - genetics; Clostridium butyricum - metabolism; Diffusion; DNA, Single-Stranded - chemistry; DNA, Single-Stranded - genetics; DNA, Single-Stranded - metabolism; Eukaryotes; Fluorescence resonance energy transfer; Fluorescence Resonance Energy Transfer - methods; Gene expression; Gene regulation; Humans; Kinetics; Microscopy, Fluorescence - methods; Modelling; Prokaryotes; Protein Binding; Protein Structure, Secondary; Proteins; RNA - chemistry; RNA - genetics; RNA - metabolism; Searching; Single Molecule Imaging - methods; Substrates
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-019-12415-y

Argonaute (Ago) proteins are key players in both gene regulation (eukaryotes) and host defense (prokaryotes). Acting on single-stranded nucleic-acid substrates, Ago relies on base pairing between a small nucleic-acid guide and its complementary target sequences for specificity. To efficiently scan nucleic-acid chains for targets, Ago diffuses laterally along the substrate and must bypass secondary structures as well as protein barriers. Using single-molecule FRET in conjunction with kinetic modelling, we reveal that target scanning is mediated through loose protein-nucleic acid interactions, allowing Ago to slide short distances over secondary structures, as well as to bypass protein barriers via intersegmental transfer. Our combined single-molecule experiment and kinetic modelling approach may serve as a platform to dissect search processes and study the effect of sequence on search kinetics for other nucleic acid-guided proteins.