Argonaute bypasses cellular obstacles without hindrance during target search

Tao Ju Cui, Misha Klein, Jorrit W. Hegge, Stanley D. Chandradoss, John van der Oost, Martin Depken*, Chirlmin Joo

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

Abstract

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.

Original languageEnglish
Article number4390
JournalNature Communications
Volume10
DOIs
Publication statusPublished - 26 Sep 2019

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bypasses
nucleic acids
Nucleic Acids
proteins
Kinetics
kinetics
Proteins
Argonaute Proteins
prokaryotes
eukaryotes
Molecules
gene expression
Substrates
Eukaryota
chutes
Gene expression
Base Pairing
molecules
platforms
Scanning

Cite this

Cui, Tao Ju ; Klein, Misha ; Hegge, Jorrit W. ; Chandradoss, Stanley D. ; van der Oost, John ; Depken, Martin ; Joo, Chirlmin. / Argonaute bypasses cellular obstacles without hindrance during target search. In: Nature Communications. 2019 ; Vol. 10.
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Argonaute bypasses cellular obstacles without hindrance during target search. / Cui, Tao Ju; Klein, Misha; Hegge, Jorrit W.; Chandradoss, Stanley D.; van der Oost, John; Depken, Martin; Joo, Chirlmin.

In: Nature Communications, Vol. 10, 4390, 26.09.2019.

Research output: Contribution to journalArticleAcademicpeer-review

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AU - Cui, Tao Ju

AU - Klein, Misha

AU - Hegge, Jorrit W.

AU - Chandradoss, Stanley D.

AU - van der Oost, John

AU - Depken, Martin

AU - Joo, Chirlmin

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AB - 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.

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