High-resolution fleezers reveal duplex opening and stepwise assembly by an oligomer of the DEAD-box helicase Ded1p
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...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2025-01-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-024-54955-y |
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| author | Eric M. Patrick Rajeev Yadav Kasun Senanayake Kyle Cotter Andrea A. Putnam Eckhard Jankowsky Matthew J. Comstock |
| author_facet | Eric M. Patrick Rajeev Yadav Kasun Senanayake Kyle Cotter Andrea A. Putnam Eckhard Jankowsky Matthew J. Comstock |
| author_sort | Eric M. Patrick |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-16013bb7d38247039ec9ab99eb1e48f8 |
| institution | Kabale University |
| issn | 2041-1723 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj-art-16013bb7d38247039ec9ab99eb1e48f82025-01-26T12:41:19ZengNature PortfolioNature Communications2041-17232025-01-0116111110.1038/s41467-024-54955-yHigh-resolution fleezers reveal duplex opening and stepwise assembly by an oligomer of the DEAD-box helicase Ded1pEric M. Patrick0Rajeev Yadav1Kasun Senanayake2Kyle Cotter3Andrea A. Putnam4Eckhard Jankowsky5Matthew J. Comstock6Department of Physics and Astronomy, Michigan State UniversityDepartment of Physics and Astronomy, Michigan State UniversityDepartment of Physics and Astronomy, Michigan State UniversityDepartment of Physics and Astronomy, Michigan State UniversityDepartment of Biochemistry and Center for RNA Science and Therapeutics, Case Western UniversityDepartment of Biochemistry and Center for RNA Science and Therapeutics, Case Western UniversityDepartment of Physics and Astronomy, Michigan State UniversityAbstract 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.https://doi.org/10.1038/s41467-024-54955-y |
| spellingShingle | Eric M. Patrick Rajeev Yadav Kasun Senanayake Kyle Cotter Andrea A. Putnam Eckhard Jankowsky Matthew J. Comstock High-resolution fleezers reveal duplex opening and stepwise assembly by an oligomer of the DEAD-box helicase Ded1p Nature Communications |
| title | High-resolution fleezers reveal duplex opening and stepwise assembly by an oligomer of the DEAD-box helicase Ded1p |
| title_full | High-resolution fleezers reveal duplex opening and stepwise assembly by an oligomer of the DEAD-box helicase Ded1p |
| title_fullStr | High-resolution fleezers reveal duplex opening and stepwise assembly by an oligomer of the DEAD-box helicase Ded1p |
| title_full_unstemmed | High-resolution fleezers reveal duplex opening and stepwise assembly by an oligomer of the DEAD-box helicase Ded1p |
| title_short | High-resolution fleezers reveal duplex opening and stepwise assembly by an oligomer of the DEAD-box helicase Ded1p |
| title_sort | high resolution fleezers reveal duplex opening and stepwise assembly by an oligomer of the dead box helicase ded1p |
| url | https://doi.org/10.1038/s41467-024-54955-y |
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