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  High-resolution fleezers reveal duplex opening and stepwise assembly by an oligomer of the DEAD-box helicase Ded1p

Patrick, E. M., Yadav, R., Senanayake, K., Cotter, K., Putnam, A. A., Jankowsky, E., et al. (2025). High-resolution fleezers reveal duplex opening and stepwise assembly by an oligomer of the DEAD-box helicase Ded1p. Nature Communications, 16: 1015. doi:10.1038/s41467-024-54955-y.

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Item Permalink: https://hdl.handle.net/21.11116/0000-0010-EBA7-9 Version Permalink: https://hdl.handle.net/21.11116/0000-0010-EBA8-8
Genre: Journal Article

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10.1038_s41467-024-54955-y.pdf (Publisher version), 2MB
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2025
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 Creators:
Patrick, Eric M.1, Author
Yadav, Rajeev2, Author
Senanayake, Kasun2, Author
Cotter, Kyle2, Author
Putnam, Andrea A.2, Author
Jankowsky, Eckhard2, Author
Comstock, Matthew J.2, Author
Affiliations:
1Department of Biological Physics, Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society, ou_persistent22              
2External Organizations, ou_persistent22              

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Free keywords: Enzyme mechanisms, Molecular biophysics, Single-molecule biophysics
 Abstract: DEAD-box RNA-dependent ATPases are ubiquitous in all domains of life where they bind and remodel RNA and RNA-protein complexes. DEAD-box ATPases with helicase activity unwind RNA duplexes by local opening of helical regions without directional movement through the duplexes and some of these enzymes, including Ded1p from Saccharomyces cerevisiae, oligomerize to effectively unwind RNA duplexes. Whether and how DEAD-box helicases coordinate oligomerization and unwinding is not known and it is unclear how many base pairs are actively opened. Using high-resolution optical tweezers and fluorescence, we reveal a highly dynamic and stochastic process of multiple Ded1p protomers assembling on and unwinding an RNA duplex. One Ded1p protomer binds to a duplex-adjacent ssRNA tail and promotes binding and subsequent unwinding of the duplex by additional Ded1p protomers in 4–6 bp steps. The data also reveal rapid duplex unwinding and rezipping linked with binding and dissociation of individual protomers and coordinated with the ATP hydrolysis cycle.

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Language(s): eng - English
 Dates: 2025-01-25
 Publication Status: Published online
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Type: Peer
 Identifiers: DOI: 10.1038/s41467-024-54955-y
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Title: Nature Communications
  Other : Nat Commun
  Abbreviation : Nat Commun
Source Genre: Journal
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Publ. Info: London : Nature Publishing Group
Pages: - Volume / Issue: 16 Sequence Number: 1015 Start / End Page: - Identifier: ISSN: 2041-1723
CoNE: https://pure.mpg.de/cone/journals/resource/2041-1723