Loading…
Domain III of the T. thermophilus 23S rRNA folds independently to a near-native state
The three-dimensional structure of the ribosomal large subunit (LSU) reveals a single morphological element, although the 23S rRNA is contained in six secondary structure domains. Based upon maps of inter- and intra-domain interactions and proposed evolutionary pathways of development, we hypothesiz...
Saved in:
Published in: | RNA (Cambridge) 2012-04, Vol.18 (4), p.752-758 |
---|---|
Main Authors: | , , , , , , , , , , |
Format: | Article |
Language: | English |
Subjects: | |
Citations: | Items that this one cites Items that cite this one |
Online Access: | Get full text |
Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
cited_by | cdi_FETCH-LOGICAL-c422t-5523c25ad904b66fff46aae3c3ba656224988cb544501da34e2c3ca82261ca9f3 |
---|---|
cites | cdi_FETCH-LOGICAL-c422t-5523c25ad904b66fff46aae3c3ba656224988cb544501da34e2c3ca82261ca9f3 |
container_end_page | 758 |
container_issue | 4 |
container_start_page | 752 |
container_title | RNA (Cambridge) |
container_volume | 18 |
creator | Athavale, Shreyas S Gossett, J Jared Hsiao, Chiaolong Bowman, Jessica C O'Neill, Eric Hershkovitz, Eli Preeprem, Thanawadee Hud, Nicholas V Wartell, Roger M Harvey, Stephen C Williams, Loren Dean |
description | The three-dimensional structure of the ribosomal large subunit (LSU) reveals a single morphological element, although the 23S rRNA is contained in six secondary structure domains. Based upon maps of inter- and intra-domain interactions and proposed evolutionary pathways of development, we hypothesize that Domain III is a truly independent structural domain of the LSU. Domain III is primarily stabilized by intra-domain interactions, negligibly perturbed by inter-domain interactions, and is not penetrated by ribosomal proteins or other rRNA. We have probed the structure of Domain III rRNA alone and when contained within the intact 23S rRNA using SHAPE (selective 2'-hydroxyl acylation analyzed by primer extension), in the absence and presence of magnesium. The combined results support the hypothesis that Domain III alone folds to a near-native state with secondary structure, intra-domain tertiary interactions, and inter-domain interactions that are independent of whether or not it is embedded in the intact 23S rRNA or within the LSU. The data presented support previous suggestions that Domain III was added relatively late in ribosomal evolution. |
doi_str_mv | 10.1261/rna.030692.111 |
format | article |
fullrecord | <record><control><sourceid>proquest_pubme</sourceid><recordid>TN_cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_3312562</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>1008833349</sourcerecordid><originalsourceid>FETCH-LOGICAL-c422t-5523c25ad904b66fff46aae3c3ba656224988cb544501da34e2c3ca82261ca9f3</originalsourceid><addsrcrecordid>eNp9kctPxCAQxonR-L56NNz00goMYLmYGJ-bGE18nMkspW5NW1bomvjfi1k1evHCEOabj5n5EbLHWcmF5kdxwJIB00aUnPMVssmlNoVhjK_mOyhVVFCJDbKV0kt-hJxeJxtCAMhjZTbJ03nosR3oZDKhoaHjzNPH8jPEPsxnbbdIVMADjfe3p7QJXZ1oO9R-7vMxjN07HQNFOniMxYBj--ZpGnH0O2StwS753a-4TZ4uLx7Proubu6vJ2elN4aQQY6GUACcU1obJqdZN00iN6MHBFLXSQkhTVW6qpFSM1wjSCwcOK5End2ga2CYnS9_5Ytr72uWeInZ2Htse47sN2Nq_maGd2efwZgG4yB9kg4MvgxheFz6Ntm-T812Hgw-LZI0wimk4rrLy8F8lZ6yqIK_VZGm5lLoYUoq--WmIM_tJzWZqdknNZmq5YP_3GD_yb0zwAZUQkkk</addsrcrecordid><sourcetype>Open Access Repository</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>1008833349</pqid></control><display><type>article</type><title>Domain III of the T. thermophilus 23S rRNA folds independently to a near-native state</title><source>PubMed Central</source><creator>Athavale, Shreyas S ; Gossett, J Jared ; Hsiao, Chiaolong ; Bowman, Jessica C ; O'Neill, Eric ; Hershkovitz, Eli ; Preeprem, Thanawadee ; Hud, Nicholas V ; Wartell, Roger M ; Harvey, Stephen C ; Williams, Loren Dean</creator><creatorcontrib>Athavale, Shreyas S ; Gossett, J Jared ; Hsiao, Chiaolong ; Bowman, Jessica C ; O'Neill, Eric ; Hershkovitz, Eli ; Preeprem, Thanawadee ; Hud, Nicholas V ; Wartell, Roger M ; Harvey, Stephen C ; Williams, Loren Dean</creatorcontrib><description>The three-dimensional structure of the ribosomal large subunit (LSU) reveals a single morphological element, although the 23S rRNA is contained in six secondary structure domains. Based upon maps of inter- and intra-domain interactions and proposed evolutionary pathways of development, we hypothesize that Domain III is a truly independent structural domain of the LSU. Domain III is primarily stabilized by intra-domain interactions, negligibly perturbed by inter-domain interactions, and is not penetrated by ribosomal proteins or other rRNA. We have probed the structure of Domain III rRNA alone and when contained within the intact 23S rRNA using SHAPE (selective 2'-hydroxyl acylation analyzed by primer extension), in the absence and presence of magnesium. The combined results support the hypothesis that Domain III alone folds to a near-native state with secondary structure, intra-domain tertiary interactions, and inter-domain interactions that are independent of whether or not it is embedded in the intact 23S rRNA or within the LSU. The data presented support previous suggestions that Domain III was added relatively late in ribosomal evolution.</description><identifier>ISSN: 1355-8382</identifier><identifier>EISSN: 1469-9001</identifier><identifier>DOI: 10.1261/rna.030692.111</identifier><identifier>PMID: 22334759</identifier><language>eng</language><publisher>United States: Cold Spring Harbor Laboratory Press</publisher><subject>Nucleic Acid Conformation ; RNA, Ribosomal, 23S - genetics ; Thermus thermophilus - genetics</subject><ispartof>RNA (Cambridge), 2012-04, Vol.18 (4), p.752-758</ispartof><rights>Copyright © 2012 RNA Society 2012</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c422t-5523c25ad904b66fff46aae3c3ba656224988cb544501da34e2c3ca82261ca9f3</citedby><cites>FETCH-LOGICAL-c422t-5523c25ad904b66fff46aae3c3ba656224988cb544501da34e2c3ca82261ca9f3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3312562/pdf/$$EPDF$$P50$$Gpubmedcentral$$H</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3312562/$$EHTML$$P50$$Gpubmedcentral$$H</linktohtml><link.rule.ids>230,315,733,786,790,891,27957,27958,53827,53829</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/22334759$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Athavale, Shreyas S</creatorcontrib><creatorcontrib>Gossett, J Jared</creatorcontrib><creatorcontrib>Hsiao, Chiaolong</creatorcontrib><creatorcontrib>Bowman, Jessica C</creatorcontrib><creatorcontrib>O'Neill, Eric</creatorcontrib><creatorcontrib>Hershkovitz, Eli</creatorcontrib><creatorcontrib>Preeprem, Thanawadee</creatorcontrib><creatorcontrib>Hud, Nicholas V</creatorcontrib><creatorcontrib>Wartell, Roger M</creatorcontrib><creatorcontrib>Harvey, Stephen C</creatorcontrib><creatorcontrib>Williams, Loren Dean</creatorcontrib><title>Domain III of the T. thermophilus 23S rRNA folds independently to a near-native state</title><title>RNA (Cambridge)</title><addtitle>RNA</addtitle><description>The three-dimensional structure of the ribosomal large subunit (LSU) reveals a single morphological element, although the 23S rRNA is contained in six secondary structure domains. Based upon maps of inter- and intra-domain interactions and proposed evolutionary pathways of development, we hypothesize that Domain III is a truly independent structural domain of the LSU. Domain III is primarily stabilized by intra-domain interactions, negligibly perturbed by inter-domain interactions, and is not penetrated by ribosomal proteins or other rRNA. We have probed the structure of Domain III rRNA alone and when contained within the intact 23S rRNA using SHAPE (selective 2'-hydroxyl acylation analyzed by primer extension), in the absence and presence of magnesium. The combined results support the hypothesis that Domain III alone folds to a near-native state with secondary structure, intra-domain tertiary interactions, and inter-domain interactions that are independent of whether or not it is embedded in the intact 23S rRNA or within the LSU. The data presented support previous suggestions that Domain III was added relatively late in ribosomal evolution.</description><subject>Nucleic Acid Conformation</subject><subject>RNA, Ribosomal, 23S - genetics</subject><subject>Thermus thermophilus - genetics</subject><issn>1355-8382</issn><issn>1469-9001</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2012</creationdate><recordtype>article</recordtype><recordid>eNp9kctPxCAQxonR-L56NNz00goMYLmYGJ-bGE18nMkspW5NW1bomvjfi1k1evHCEOabj5n5EbLHWcmF5kdxwJIB00aUnPMVssmlNoVhjK_mOyhVVFCJDbKV0kt-hJxeJxtCAMhjZTbJ03nosR3oZDKhoaHjzNPH8jPEPsxnbbdIVMADjfe3p7QJXZ1oO9R-7vMxjN07HQNFOniMxYBj--ZpGnH0O2StwS753a-4TZ4uLx7Proubu6vJ2elN4aQQY6GUACcU1obJqdZN00iN6MHBFLXSQkhTVW6qpFSM1wjSCwcOK5End2ga2CYnS9_5Ytr72uWeInZ2Htse47sN2Nq_maGd2efwZgG4yB9kg4MvgxheFz6Ntm-T812Hgw-LZI0wimk4rrLy8F8lZ6yqIK_VZGm5lLoYUoq--WmIM_tJzWZqdknNZmq5YP_3GD_yb0zwAZUQkkk</recordid><startdate>20120401</startdate><enddate>20120401</enddate><creator>Athavale, Shreyas S</creator><creator>Gossett, J Jared</creator><creator>Hsiao, Chiaolong</creator><creator>Bowman, Jessica C</creator><creator>O'Neill, Eric</creator><creator>Hershkovitz, Eli</creator><creator>Preeprem, Thanawadee</creator><creator>Hud, Nicholas V</creator><creator>Wartell, Roger M</creator><creator>Harvey, Stephen C</creator><creator>Williams, Loren Dean</creator><general>Cold Spring Harbor Laboratory Press</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7TM</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20120401</creationdate><title>Domain III of the T. thermophilus 23S rRNA folds independently to a near-native state</title><author>Athavale, Shreyas S ; Gossett, J Jared ; Hsiao, Chiaolong ; Bowman, Jessica C ; O'Neill, Eric ; Hershkovitz, Eli ; Preeprem, Thanawadee ; Hud, Nicholas V ; Wartell, Roger M ; Harvey, Stephen C ; Williams, Loren Dean</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c422t-5523c25ad904b66fff46aae3c3ba656224988cb544501da34e2c3ca82261ca9f3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2012</creationdate><topic>Nucleic Acid Conformation</topic><topic>RNA, Ribosomal, 23S - genetics</topic><topic>Thermus thermophilus - genetics</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Athavale, Shreyas S</creatorcontrib><creatorcontrib>Gossett, J Jared</creatorcontrib><creatorcontrib>Hsiao, Chiaolong</creatorcontrib><creatorcontrib>Bowman, Jessica C</creatorcontrib><creatorcontrib>O'Neill, Eric</creatorcontrib><creatorcontrib>Hershkovitz, Eli</creatorcontrib><creatorcontrib>Preeprem, Thanawadee</creatorcontrib><creatorcontrib>Hud, Nicholas V</creatorcontrib><creatorcontrib>Wartell, Roger M</creatorcontrib><creatorcontrib>Harvey, Stephen C</creatorcontrib><creatorcontrib>Williams, Loren Dean</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Nucleic Acids Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>RNA (Cambridge)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Athavale, Shreyas S</au><au>Gossett, J Jared</au><au>Hsiao, Chiaolong</au><au>Bowman, Jessica C</au><au>O'Neill, Eric</au><au>Hershkovitz, Eli</au><au>Preeprem, Thanawadee</au><au>Hud, Nicholas V</au><au>Wartell, Roger M</au><au>Harvey, Stephen C</au><au>Williams, Loren Dean</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Domain III of the T. thermophilus 23S rRNA folds independently to a near-native state</atitle><jtitle>RNA (Cambridge)</jtitle><addtitle>RNA</addtitle><date>2012-04-01</date><risdate>2012</risdate><volume>18</volume><issue>4</issue><spage>752</spage><epage>758</epage><pages>752-758</pages><issn>1355-8382</issn><eissn>1469-9001</eissn><notes>ObjectType-Article-2</notes><notes>SourceType-Scholarly Journals-1</notes><notes>ObjectType-Feature-1</notes><notes>content type line 23</notes><notes>ObjectType-Article-1</notes><notes>ObjectType-Feature-2</notes><abstract>The three-dimensional structure of the ribosomal large subunit (LSU) reveals a single morphological element, although the 23S rRNA is contained in six secondary structure domains. Based upon maps of inter- and intra-domain interactions and proposed evolutionary pathways of development, we hypothesize that Domain III is a truly independent structural domain of the LSU. Domain III is primarily stabilized by intra-domain interactions, negligibly perturbed by inter-domain interactions, and is not penetrated by ribosomal proteins or other rRNA. We have probed the structure of Domain III rRNA alone and when contained within the intact 23S rRNA using SHAPE (selective 2'-hydroxyl acylation analyzed by primer extension), in the absence and presence of magnesium. The combined results support the hypothesis that Domain III alone folds to a near-native state with secondary structure, intra-domain tertiary interactions, and inter-domain interactions that are independent of whether or not it is embedded in the intact 23S rRNA or within the LSU. The data presented support previous suggestions that Domain III was added relatively late in ribosomal evolution.</abstract><cop>United States</cop><pub>Cold Spring Harbor Laboratory Press</pub><pmid>22334759</pmid><doi>10.1261/rna.030692.111</doi><tpages>7</tpages><oa>free_for_read</oa></addata></record> |
fulltext | fulltext |
identifier | ISSN: 1355-8382 |
ispartof | RNA (Cambridge), 2012-04, Vol.18 (4), p.752-758 |
issn | 1355-8382 1469-9001 |
language | eng |
recordid | cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_3312562 |
source | PubMed Central |
subjects | Nucleic Acid Conformation RNA, Ribosomal, 23S - genetics Thermus thermophilus - genetics |
title | Domain III of the T. thermophilus 23S rRNA folds independently to a near-native state |
url | http://sfxeu10.hosted.exlibrisgroup.com/loughborough?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-09-22T01%3A26%3A41IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_pubme&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Domain%20III%20of%20the%20T.%20thermophilus%2023S%20rRNA%20folds%20independently%20to%20a%20near-native%20state&rft.jtitle=RNA%20(Cambridge)&rft.au=Athavale,%20Shreyas%20S&rft.date=2012-04-01&rft.volume=18&rft.issue=4&rft.spage=752&rft.epage=758&rft.pages=752-758&rft.issn=1355-8382&rft.eissn=1469-9001&rft_id=info:doi/10.1261/rna.030692.111&rft_dat=%3Cproquest_pubme%3E1008833349%3C/proquest_pubme%3E%3Cgrp_id%3Ecdi_FETCH-LOGICAL-c422t-5523c25ad904b66fff46aae3c3ba656224988cb544501da34e2c3ca82261ca9f3%3C/grp_id%3E%3Coa%3E%3C/oa%3E%3Curl%3E%3C/url%3E&rft_id=info:oai/&rft_pqid=1008833349&rft_id=info:pmid/22334759&rfr_iscdi=true |