Loading…
Mechanistic analysis of Riboswitch Ligand interactions provides insights into pharmacological control over gene expression
Riboswitches are structured RNA elements that regulate gene expression upon binding to small molecule ligands. Understanding the mechanisms by which small molecules impact riboswitch activity is key to developing potent, selective ligands for these and other RNA targets. We report the structure-info...
Saved in:
| Published in: | Nature communications 2024-01, Vol.15 (1), p.8173 |
|---|---|
| Main Authors: | , , , , , , , , , , , , |
| Format: | Article |
| Language: | English |
| Subjects: | |
| Online Access: | Get full text |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| cited_by | |
|---|---|
| cites | |
| container_end_page | |
| container_issue | 1 |
| container_start_page | 8173 |
| container_title | Nature communications |
| container_volume | 15 |
| creator | Parmar, Shaifaly Bume, Desta Doro Connelly, Colleen M Boer, Robert E Prestwood, Peri R Wang, Zhen Labuhn, Henning Sinnadurai, Krishshanthi Feri, Adeline Ouellet, Jimmy Homan, Philip Numata, Tomoyuki Schneekloth, John S |
| description | Riboswitches are structured RNA elements that regulate gene expression upon binding to small molecule ligands. Understanding the mechanisms by which small molecules impact riboswitch activity is key to developing potent, selective ligands for these and other RNA targets. We report the structure-informed design of chemically diverse synthetic ligands for PreQ1 riboswitches. Multiple X-ray co-crystal structures of synthetic ligands with the Thermoanaerobacter tengcongensis (Tte)-PreQ1 riboswitch confirm a common binding site with the cognate ligand, despite considerable chemical differences among the ligands. Structure probing assays demonstrate that one ligand causes conformational changes similar to PreQ1 in six structurally and mechanistically diverse PreQ1 riboswitch aptamers. Single-molecule force spectroscopy is used to demonstrate differential modes of riboswitch stabilization by the ligands. Binding of the natural ligand brings about the formation of a persistent, folded pseudoknot structure, whereas a synthetic ligand decreases the rate of unfolding through a kinetic mechanism. Single round transcription termination assays show the biochemical activity of the ligands, while a GFP reporter system reveals compound activity in regulating gene expression in live cells without toxicity. Taken together, this study reveals that diverse small molecules can impact gene expression in live cells by altering conformational changes in RNA structures through distinct mechanisms.Riboswitches are structured RNA elements that regulate gene expression upon binding to small molecule ligands. Here the authors report the discovery and characterization of a series of small molecule ligands for the PreQ1 riboswitch. |
| doi_str_mv | 10.1038/s41467-024-52235-3 |
| format | article |
| fullrecord | <record><control><sourceid>proquest</sourceid><recordid>TN_cdi_proquest_journals_3106221284</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>3106221284</sourcerecordid><originalsourceid>FETCH-proquest_journals_31062212843</originalsourceid><addsrcrecordid>eNqNjs1KA0EQhAdBMGhewFOD59H5S7KeRfGgF8k9jJPObodxep2exJ-ndwUfwLpUURQfpdSlNdfW-O5Ggg3LlTYu6IVzfqH9iZo5E6y2K-fP1Fxkbyb5W9uFMFPfz5iGWEgaJYgl5i8hAd7BC72yfFBLAzxRH8sWqDSsMTXiIjBWPtIWZWqF-qH9hsYwDrG-xcSZe0oxQ-LSKmfgI1bosSDg51hRZIJcqNNdzILzPz9XVw_367tHPbHfDyhts-dDnS7JxluzdM66Lvj_rX4AqehVww</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>3106221284</pqid></control><display><type>article</type><title>Mechanistic analysis of Riboswitch Ligand interactions provides insights into pharmacological control over gene expression</title><source>Publicly Available Content Database</source><source>Springer Nature - Connect here FIRST to enable access</source><source>PubMed Central</source><source>Springer Nature - nature.com Journals - Fully Open Access</source><creator>Parmar, Shaifaly ; Bume, Desta Doro ; Connelly, Colleen M ; Boer, Robert E ; Prestwood, Peri R ; Wang, Zhen ; Labuhn, Henning ; Sinnadurai, Krishshanthi ; Feri, Adeline ; Ouellet, Jimmy ; Homan, Philip ; Numata, Tomoyuki ; Schneekloth, John S</creator><creatorcontrib>Parmar, Shaifaly ; Bume, Desta Doro ; Connelly, Colleen M ; Boer, Robert E ; Prestwood, Peri R ; Wang, Zhen ; Labuhn, Henning ; Sinnadurai, Krishshanthi ; Feri, Adeline ; Ouellet, Jimmy ; Homan, Philip ; Numata, Tomoyuki ; Schneekloth, John S</creatorcontrib><description>Riboswitches are structured RNA elements that regulate gene expression upon binding to small molecule ligands. Understanding the mechanisms by which small molecules impact riboswitch activity is key to developing potent, selective ligands for these and other RNA targets. We report the structure-informed design of chemically diverse synthetic ligands for PreQ1 riboswitches. Multiple X-ray co-crystal structures of synthetic ligands with the Thermoanaerobacter tengcongensis (Tte)-PreQ1 riboswitch confirm a common binding site with the cognate ligand, despite considerable chemical differences among the ligands. Structure probing assays demonstrate that one ligand causes conformational changes similar to PreQ1 in six structurally and mechanistically diverse PreQ1 riboswitch aptamers. Single-molecule force spectroscopy is used to demonstrate differential modes of riboswitch stabilization by the ligands. Binding of the natural ligand brings about the formation of a persistent, folded pseudoknot structure, whereas a synthetic ligand decreases the rate of unfolding through a kinetic mechanism. Single round transcription termination assays show the biochemical activity of the ligands, while a GFP reporter system reveals compound activity in regulating gene expression in live cells without toxicity. Taken together, this study reveals that diverse small molecules can impact gene expression in live cells by altering conformational changes in RNA structures through distinct mechanisms.Riboswitches are structured RNA elements that regulate gene expression upon binding to small molecule ligands. Here the authors report the discovery and characterization of a series of small molecule ligands for the PreQ1 riboswitch.</description><identifier>EISSN: 2041-1723</identifier><identifier>DOI: 10.1038/s41467-024-52235-3</identifier><language>eng</language><publisher>London: Nature Publishing Group</publisher><subject>Aptamers ; Binding sites ; Chemical activity ; Gene expression ; Impact analysis ; Ligands ; Molecular structure ; Ribonucleic acid ; Riboswitches ; RNA ; Spectroscopy ; Toxicity ; Transcription termination</subject><ispartof>Nature communications, 2024-01, Vol.15 (1), p.8173</ispartof><rights>This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply 2024. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.proquest.com/docview/3106221284/fulltextPDF?pq-origsite=primo$$EPDF$$P50$$Gproquest$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.proquest.com/docview/3106221284?pq-origsite=primo$$EHTML$$P50$$Gproquest$$Hfree_for_read</linktohtml><link.rule.ids>315,786,790,25783,27957,27958,37047,44625,75483</link.rule.ids></links><search><creatorcontrib>Parmar, Shaifaly</creatorcontrib><creatorcontrib>Bume, Desta Doro</creatorcontrib><creatorcontrib>Connelly, Colleen M</creatorcontrib><creatorcontrib>Boer, Robert E</creatorcontrib><creatorcontrib>Prestwood, Peri R</creatorcontrib><creatorcontrib>Wang, Zhen</creatorcontrib><creatorcontrib>Labuhn, Henning</creatorcontrib><creatorcontrib>Sinnadurai, Krishshanthi</creatorcontrib><creatorcontrib>Feri, Adeline</creatorcontrib><creatorcontrib>Ouellet, Jimmy</creatorcontrib><creatorcontrib>Homan, Philip</creatorcontrib><creatorcontrib>Numata, Tomoyuki</creatorcontrib><creatorcontrib>Schneekloth, John S</creatorcontrib><title>Mechanistic analysis of Riboswitch Ligand interactions provides insights into pharmacological control over gene expression</title><title>Nature communications</title><description>Riboswitches are structured RNA elements that regulate gene expression upon binding to small molecule ligands. Understanding the mechanisms by which small molecules impact riboswitch activity is key to developing potent, selective ligands for these and other RNA targets. We report the structure-informed design of chemically diverse synthetic ligands for PreQ1 riboswitches. Multiple X-ray co-crystal structures of synthetic ligands with the Thermoanaerobacter tengcongensis (Tte)-PreQ1 riboswitch confirm a common binding site with the cognate ligand, despite considerable chemical differences among the ligands. Structure probing assays demonstrate that one ligand causes conformational changes similar to PreQ1 in six structurally and mechanistically diverse PreQ1 riboswitch aptamers. Single-molecule force spectroscopy is used to demonstrate differential modes of riboswitch stabilization by the ligands. Binding of the natural ligand brings about the formation of a persistent, folded pseudoknot structure, whereas a synthetic ligand decreases the rate of unfolding through a kinetic mechanism. Single round transcription termination assays show the biochemical activity of the ligands, while a GFP reporter system reveals compound activity in regulating gene expression in live cells without toxicity. Taken together, this study reveals that diverse small molecules can impact gene expression in live cells by altering conformational changes in RNA structures through distinct mechanisms.Riboswitches are structured RNA elements that regulate gene expression upon binding to small molecule ligands. Here the authors report the discovery and characterization of a series of small molecule ligands for the PreQ1 riboswitch.</description><subject>Aptamers</subject><subject>Binding sites</subject><subject>Chemical activity</subject><subject>Gene expression</subject><subject>Impact analysis</subject><subject>Ligands</subject><subject>Molecular structure</subject><subject>Ribonucleic acid</subject><subject>Riboswitches</subject><subject>RNA</subject><subject>Spectroscopy</subject><subject>Toxicity</subject><subject>Transcription termination</subject><issn>2041-1723</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2024</creationdate><recordtype>article</recordtype><sourceid>PIMPY</sourceid><recordid>eNqNjs1KA0EQhAdBMGhewFOD59H5S7KeRfGgF8k9jJPObodxep2exJ-ndwUfwLpUURQfpdSlNdfW-O5Ggg3LlTYu6IVzfqH9iZo5E6y2K-fP1Fxkbyb5W9uFMFPfz5iGWEgaJYgl5i8hAd7BC72yfFBLAzxRH8sWqDSsMTXiIjBWPtIWZWqF-qH9hsYwDrG-xcSZe0oxQ-LSKmfgI1bosSDg51hRZIJcqNNdzILzPz9XVw_367tHPbHfDyhts-dDnS7JxluzdM66Lvj_rX4AqehVww</recordid><startdate>20240101</startdate><enddate>20240101</enddate><creator>Parmar, Shaifaly</creator><creator>Bume, Desta Doro</creator><creator>Connelly, Colleen M</creator><creator>Boer, Robert E</creator><creator>Prestwood, Peri R</creator><creator>Wang, Zhen</creator><creator>Labuhn, Henning</creator><creator>Sinnadurai, Krishshanthi</creator><creator>Feri, Adeline</creator><creator>Ouellet, Jimmy</creator><creator>Homan, Philip</creator><creator>Numata, Tomoyuki</creator><creator>Schneekloth, John S</creator><general>Nature Publishing Group</general><scope>3V.</scope><scope>7QL</scope><scope>7QP</scope><scope>7QR</scope><scope>7SN</scope><scope>7SS</scope><scope>7ST</scope><scope>7T5</scope><scope>7T7</scope><scope>7TM</scope><scope>7TO</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M7P</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>RC3</scope><scope>SOI</scope></search><sort><creationdate>20240101</creationdate><title>Mechanistic analysis of Riboswitch Ligand interactions provides insights into pharmacological control over gene expression</title><author>Parmar, Shaifaly ; Bume, Desta Doro ; Connelly, Colleen M ; Boer, Robert E ; Prestwood, Peri R ; Wang, Zhen ; Labuhn, Henning ; Sinnadurai, Krishshanthi ; Feri, Adeline ; Ouellet, Jimmy ; Homan, Philip ; Numata, Tomoyuki ; Schneekloth, John S</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-proquest_journals_31062212843</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2024</creationdate><topic>Aptamers</topic><topic>Binding sites</topic><topic>Chemical activity</topic><topic>Gene expression</topic><topic>Impact analysis</topic><topic>Ligands</topic><topic>Molecular structure</topic><topic>Ribonucleic acid</topic><topic>Riboswitches</topic><topic>RNA</topic><topic>Spectroscopy</topic><topic>Toxicity</topic><topic>Transcription termination</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Parmar, Shaifaly</creatorcontrib><creatorcontrib>Bume, Desta Doro</creatorcontrib><creatorcontrib>Connelly, Colleen M</creatorcontrib><creatorcontrib>Boer, Robert E</creatorcontrib><creatorcontrib>Prestwood, Peri R</creatorcontrib><creatorcontrib>Wang, Zhen</creatorcontrib><creatorcontrib>Labuhn, Henning</creatorcontrib><creatorcontrib>Sinnadurai, Krishshanthi</creatorcontrib><creatorcontrib>Feri, Adeline</creatorcontrib><creatorcontrib>Ouellet, Jimmy</creatorcontrib><creatorcontrib>Homan, Philip</creatorcontrib><creatorcontrib>Numata, Tomoyuki</creatorcontrib><creatorcontrib>Schneekloth, John S</creatorcontrib><collection>ProQuest Central (Corporate)</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Calcium & Calcified Tissue Abstracts</collection><collection>Chemoreception Abstracts</collection><collection>Ecology Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Environment Abstracts</collection><collection>Immunology Abstracts</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Nucleic Acids Abstracts</collection><collection>Oncogenes and Growth Factors Abstracts</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Technology Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni)</collection><collection>ProQuest Central UK/Ireland</collection><collection>Advanced Technologies & Aerospace Collection</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Technology Collection</collection><collection>Natural Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Biological Sciences</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>PML(ProQuest Medical Library)</collection><collection>Biological Science Database</collection><collection>Advanced Technologies & Aerospace Database</collection><collection>ProQuest Advanced Technologies & Aerospace Collection</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Publicly Available Content Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>Genetics Abstracts</collection><collection>Environment Abstracts</collection><jtitle>Nature communications</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Parmar, Shaifaly</au><au>Bume, Desta Doro</au><au>Connelly, Colleen M</au><au>Boer, Robert E</au><au>Prestwood, Peri R</au><au>Wang, Zhen</au><au>Labuhn, Henning</au><au>Sinnadurai, Krishshanthi</au><au>Feri, Adeline</au><au>Ouellet, Jimmy</au><au>Homan, Philip</au><au>Numata, Tomoyuki</au><au>Schneekloth, John S</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Mechanistic analysis of Riboswitch Ligand interactions provides insights into pharmacological control over gene expression</atitle><jtitle>Nature communications</jtitle><date>2024-01-01</date><risdate>2024</risdate><volume>15</volume><issue>1</issue><spage>8173</spage><pages>8173-</pages><eissn>2041-1723</eissn><abstract>Riboswitches are structured RNA elements that regulate gene expression upon binding to small molecule ligands. Understanding the mechanisms by which small molecules impact riboswitch activity is key to developing potent, selective ligands for these and other RNA targets. We report the structure-informed design of chemically diverse synthetic ligands for PreQ1 riboswitches. Multiple X-ray co-crystal structures of synthetic ligands with the Thermoanaerobacter tengcongensis (Tte)-PreQ1 riboswitch confirm a common binding site with the cognate ligand, despite considerable chemical differences among the ligands. Structure probing assays demonstrate that one ligand causes conformational changes similar to PreQ1 in six structurally and mechanistically diverse PreQ1 riboswitch aptamers. Single-molecule force spectroscopy is used to demonstrate differential modes of riboswitch stabilization by the ligands. Binding of the natural ligand brings about the formation of a persistent, folded pseudoknot structure, whereas a synthetic ligand decreases the rate of unfolding through a kinetic mechanism. Single round transcription termination assays show the biochemical activity of the ligands, while a GFP reporter system reveals compound activity in regulating gene expression in live cells without toxicity. Taken together, this study reveals that diverse small molecules can impact gene expression in live cells by altering conformational changes in RNA structures through distinct mechanisms.Riboswitches are structured RNA elements that regulate gene expression upon binding to small molecule ligands. Here the authors report the discovery and characterization of a series of small molecule ligands for the PreQ1 riboswitch.</abstract><cop>London</cop><pub>Nature Publishing Group</pub><doi>10.1038/s41467-024-52235-3</doi><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | EISSN: 2041-1723 |
| ispartof | Nature communications, 2024-01, Vol.15 (1), p.8173 |
| issn | 2041-1723 |
| language | eng |
| recordid | cdi_proquest_journals_3106221284 |
| source | Publicly Available Content Database; Springer Nature - Connect here FIRST to enable access; PubMed Central; Springer Nature - nature.com Journals - Fully Open Access |
| subjects | Aptamers Binding sites Chemical activity Gene expression Impact analysis Ligands Molecular structure Ribonucleic acid Riboswitches RNA Spectroscopy Toxicity Transcription termination |
| title | Mechanistic analysis of Riboswitch Ligand interactions provides insights into pharmacological control over gene expression |
| url | http://sfxeu10.hosted.exlibrisgroup.com/loughborough?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-09-21T07%3A42%3A45IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Mechanistic%20analysis%20of%20Riboswitch%20Ligand%20interactions%20provides%20insights%20into%20pharmacological%20control%20over%20gene%20expression&rft.jtitle=Nature%20communications&rft.au=Parmar,%20Shaifaly&rft.date=2024-01-01&rft.volume=15&rft.issue=1&rft.spage=8173&rft.pages=8173-&rft.eissn=2041-1723&rft_id=info:doi/10.1038/s41467-024-52235-3&rft_dat=%3Cproquest%3E3106221284%3C/proquest%3E%3Cgrp_id%3Ecdi_FETCH-proquest_journals_31062212843%3C/grp_id%3E%3Coa%3E%3C/oa%3E%3Curl%3E%3C/url%3E&rft_id=info:oai/&rft_pqid=3106221284&rft_id=info:pmid/&rfr_iscdi=true |