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<!DOCTYPE html> <html lang="en" dir="ltr" xmlns="http://www.w3.org/1999/xhtml" xmlns:mml="http://www.w3.org/1998/Math/MathML"> <head prefix="og: http://ogp.me/ns# article: http://ogp.me/ns/article# book: http://ogp.me/ns/book#" >  <link rel="dns-prefetch" href="//d33xdlntwy0kbs.cloudfront.net" /> <link rel="dns-prefetch" href="//www.google.com" /> <link rel="dns-prefetch" href="//scholar.google.com" /> <link rel="dns-prefetch" href="//www.googletagmanager.com" /> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> <link rel="shortcut icon" href="https://www.biorxiv.org/sites/default/files/images/favicon.ico" type="image/vnd.microsoft.icon" /> <meta name="viewport" content="width=device-width, initial-scale=1" /> <link rel="alternate" type="application/pdf" title="Full Text (PDF)" href="/content/10.1101/078733v1.full.pdf" /> <link rel="alternate" type="text/plain" title="Full Text (Plain)" href="/content/10.1101/078733v1.full.txt" /> <meta name="article_thumbnail" content="https://www.biorxiv.org/content/biorxiv/early/2016/10/01/078733/embed/inline-graphic-1.gif" /> <meta name="type" content="article" /> <meta name="category" content="article" /> <meta name="HW.identifier" content="/biorxiv/early/2016/10/01/078733.atom" /> <meta name="HW.pisa" content="biorxiv;078733v1" /> <meta name="DC.Format" content="text/html" /> <meta name="DC.Language" content="en" /> <meta name="DC.Title" content="Crystal structure and RNA-binding properties of an Hfq homolog from the deep-branching Aquificae: Conservation of the lateral RNA-binding mode" /> <meta name="DC.Identifier" content="10.1101/078733" /> <meta name="DC.Date" content="2016-10-01" /> <meta name="DC.Publisher" content="Cold Spring Harbor Laboratory" /> <meta name="DC.Rights" content="© 2016, Posted by Cold Spring Harbor Laboratory. The copyright holder for this pre-print is the author. All rights reserved. The material may not be redistributed, re-used or adapted without the author’s permission." /> <meta name="DC.AccessRights" content="restricted" /> <meta name="DC.Description" content="Synopsis The structure of an Hfq homolog from the deep-branching thermophilic bacterium Aquifex aeolicus , determined to 1.5-Å resolution both in apo form and bound to a uridine-rich RNA, reveals a conserved, pre-organized RNA-binding pocket on the lateral rim of the Hfq hexamer. Abstract The host factor Hfq, as the bacterial branch of the Sm family, is an RNA-binding protein involved in post-transcriptional regulation of mRNA expression and turnover. Hfq facilitates pairing between small regulatory RNAs (sRNA) and their corresponding mRNA targets by binding both RNAs and bringing them into close proximity. Hfq homologs self-assemble into homo-hexameric rings, with at least two distinct surfaces that bind RNA. Recently, another binding site—dubbed the ‘lateral rim’—has been implicated in sRNA•mRNA annealing; the RNA-binding properties of this site appear to be rather subtle, and its degree of evolutionary conservation is unknown. An Hfq homolog has been identified in the phylogenetically deep-branching thermophile Aquifex aeolicus ( Aae ), but little is known about the structures and functions of Hfq from basal bacterial lineages such as the Aquificae. Thus, we have cloned, overexpressed, purified, crystallized, and biochemically characterized Aae Hfq. We have determined the structures of Aae Hfq in space-groups P 1 and P 6, both to 1.5 Å resolution, and we have discovered nanomolar-scale binding affinities for uridine- and adenosine-rich RNAs. Co-crystallization with U6 RNA reveals that the outer rim of the Aae Hfq hexamer features a well-defined binding pocket that is selective for uracil. This Aae Hfq structure, combined with biochemical and biophysical characterization of the homolog, reveals deep evolutionary conservation of the lateral RNA-binding mode, and lays a foundation for further studies of Hfq-associated RNA biology in ancient bacterial phyla." /> <meta name="DC.Contributor" content="Kimberly A Stanek" /> <meta name="DC.Contributor" content="Jennifer P West" /> <meta name="DC.Contributor" content="Peter S Randolph" /> <meta name="DC.Contributor" content="Cameron Mura" /> <meta name="article:published_time" content="2016-10-01" /> <meta name="article:section" content="New Results" /> <meta name="citation_title" content="Crystal structure and RNA-binding properties of an Hfq homolog from the deep-branching Aquificae: Conservation of the lateral RNA-binding mode" /> <meta name="citation_abstract" lang="en" content="<h3>Synopsis</h3> <p>The structure of an Hfq homolog from the deep-branching thermophilic bacterium <i>Aquifex aeolicus</i>, determined to 1.5-Å resolution both in <i>apo</i> form and bound to a uridine-rich RNA, reveals a conserved, pre-organized RNA-binding pocket on the lateral rim of the Hfq hexamer.</p><h3>Abstract</h3> <p>The host factor Hfq, as the bacterial branch of the Sm family, is an RNA-binding protein involved in post-transcriptional regulation of mRNA expression and turnover. Hfq facilitates pairing between small regulatory RNAs (sRNA) and their corresponding mRNA targets by binding both RNAs and bringing them into close proximity. Hfq homologs self-assemble into homo-hexameric rings, with at least two distinct surfaces that bind RNA. Recently, another binding site—dubbed the ‘lateral rim’—has been implicated in sRNA•mRNA annealing; the RNA-binding properties of this site appear to be rather subtle, and its degree of evolutionary conservation is unknown. An Hfq homolog has been identified in the phylogenetically deep-branching thermophile <i>Aquifex aeolicus</i> (<i>Aae</i>), but little is known about the structures and functions of Hfq from basal bacterial lineages such as the Aquificae. Thus, we have cloned, overexpressed, purified, crystallized, and biochemically characterized <i>Aae</i> Hfq. We have determined the structures of <i>Aae</i> Hfq in space-groups <i>P</i>1 and <i>P</i>6, both to 1.5 Å resolution, and we have discovered nanomolar-scale binding affinities for uridine- and adenosine-rich RNAs. Co-crystallization with U<sub>6</sub> RNA reveals that the outer rim of the <i>Aae</i> Hfq hexamer features a well-defined binding pocket that is selective for uracil. This <i>Aae</i> Hfq structure, combined with biochemical and biophysical characterization of the homolog, reveals deep evolutionary conservation of the lateral RNA-binding mode, and lays a foundation for further studies of Hfq-associated RNA biology in ancient bacterial phyla.</p>" /> <meta name="citation_journal_title" content="bioRxiv" /> <meta name="citation_publisher" content="Cold Spring Harbor Laboratory" /> <meta name="citation_publication_date" content="2016/01/01" /> <meta name="citation_mjid" content="biorxiv;078733v1" /> <meta name="citation_id" content="078733v1" /> <meta name="citation_public_url" content="https://www.biorxiv.org/content/10.1101/078733v1" /> <meta name="citation_abstract_html_url" content="https://www.biorxiv.org/content/10.1101/078733v1.abstract" /> <meta name="citation_full_html_url" content="https://www.biorxiv.org/content/10.1101/078733v1.full" /> <meta name="citation_pdf_url" content="https://www.biorxiv.org/content/biorxiv/early/2016/10/01/078733.full.pdf" /> <meta name="citation_doi" content="10.1101/078733" /> <meta name="citation_num_pages" content="44" /> <meta name="citation_article_type" content="Article" /> <meta name="citation_section" content="New Results" /> <meta name="citation_firstpage" content="078733" /> <meta name="citation_author" content="Kimberly A Stanek" /> <meta name="citation_author_institution" content="Department of Chemistry, University of Virginia" /> <meta name="citation_author" content="Jennifer P West" /> <meta name="citation_author_institution" content="Department of Chemistry, University of Virginia" /> <meta name="citation_author" content="Peter S Randolph" /> <meta name="citation_author_institution" content="Department of Chemistry, University of Virginia" /> <meta name="citation_author" content="Cameron Mura" /> <meta name="citation_author_institution" content="Department of Chemistry, University of Virginia" /> <meta name="citation_author_email" content="cmura@muralab.org" /> <meta name="citation_reference" content="Adams, P. 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Acta Crystallogr D Biol Crystallogr 66, 889–900." /> <meta name="twitter:title" content="Crystal structure and RNA-binding properties of an Hfq homolog from the deep-branching Aquificae: Conservation of the lateral RNA-binding mode" /> <meta name="twitter:site" content="@biorxivpreprint" /> <meta name="twitter:card" content="summary" /> <meta name="twitter:image" content="https://www.biorxiv.org/sites/default/files/images/biorxiv_logo_homepage7-5-small.png" /> <meta name="twitter:description" content="Synopsis The structure of an Hfq homolog from the deep-branching thermophilic bacterium Aquifex aeolicus , determined to 1.5-Å resolution both in apo form and bound to a uridine-rich RNA, reveals a conserved, pre-organized RNA-binding pocket on the lateral rim of the Hfq hexamer. Abstract The host factor Hfq, as the bacterial branch of the Sm family, is an RNA-binding protein involved in post-transcriptional regulation of mRNA expression and turnover. Hfq facilitates pairing between small regulatory RNAs (sRNA) and their corresponding mRNA targets by binding both RNAs and bringing them into close proximity. Hfq homologs self-assemble into homo-hexameric rings, with at least two distinct surfaces that bind RNA. Recently, another binding site—dubbed the ‘lateral rim’—has been implicated in sRNA•mRNA annealing; the RNA-binding properties of this site appear to be rather subtle, and its degree of evolutionary conservation is unknown. An Hfq homolog has been identified in the phylogenetically deep-branching thermophile Aquifex aeolicus ( Aae ), but little is known about the structures and functions of Hfq from basal bacterial lineages such as the Aquificae. Thus, we have cloned, overexpressed, purified, crystallized, and biochemically characterized Aae Hfq. We have determined the structures of Aae Hfq in space-groups P 1 and P 6, both to 1.5 Å resolution, and we have discovered nanomolar-scale binding affinities for uridine- and adenosine-rich RNAs. Co-crystallization with U6 RNA reveals that the outer rim of the Aae Hfq hexamer features a well-defined binding pocket that is selective for uracil. This Aae Hfq structure, combined with biochemical and biophysical characterization of the homolog, reveals deep evolutionary conservation of the lateral RNA-binding mode, and lays a foundation for further studies of Hfq-associated RNA biology in ancient bacterial phyla." /> <meta name="og-title" property="og:title" content="Crystal structure and RNA-binding properties of an Hfq homolog from the deep-branching Aquificae: Conservation of the lateral RNA-binding mode" /> <meta name="og-url" property="og:url" content="https://www.biorxiv.org/content/10.1101/078733v1" /> <meta name="og-site-name" property="og:site_name" content="bioRxiv" /> <meta name="og-description" property="og:description" content="Synopsis The structure of an Hfq homolog from the deep-branching thermophilic bacterium Aquifex aeolicus , determined to 1.5-Å resolution both in apo form and bound to a uridine-rich RNA, reveals a conserved, pre-organized RNA-binding pocket on the lateral rim of the Hfq hexamer. Abstract The host factor Hfq, as the bacterial branch of the Sm family, is an RNA-binding protein involved in post-transcriptional regulation of mRNA expression and turnover. Hfq facilitates pairing between small regulatory RNAs (sRNA) and their corresponding mRNA targets by binding both RNAs and bringing them into close proximity. Hfq homologs self-assemble into homo-hexameric rings, with at least two distinct surfaces that bind RNA. Recently, another binding site—dubbed the ‘lateral rim’—has been implicated in sRNA•mRNA annealing; the RNA-binding properties of this site appear to be rather subtle, and its degree of evolutionary conservation is unknown. An Hfq homolog has been identified in the phylogenetically deep-branching thermophile Aquifex aeolicus ( Aae ), but little is known about the structures and functions of Hfq from basal bacterial lineages such as the Aquificae. Thus, we have cloned, overexpressed, purified, crystallized, and biochemically characterized Aae Hfq. We have determined the structures of Aae Hfq in space-groups P 1 and P 6, both to 1.5 Å resolution, and we have discovered nanomolar-scale binding affinities for uridine- and adenosine-rich RNAs. Co-crystallization with U6 RNA reveals that the outer rim of the Aae Hfq hexamer features a well-defined binding pocket that is selective for uracil. This Aae Hfq structure, combined with biochemical and biophysical characterization of the homolog, reveals deep evolutionary conservation of the lateral RNA-binding mode, and lays a foundation for further studies of Hfq-associated RNA biology in ancient bacterial phyla." /> <meta name="og-type" property="og:type" content="article" /> <meta name="og-image" property="og:image" content="https://www.biorxiv.org/sites/default/files/images/biorxiv_logo_homepage7-5-small.png" /> <meta name="citation_date" content="2016-10-01" /> <link rel="alternate" type="application/vnd.ms-powerpoint" title="Powerpoint" href="/content/10.1101/078733v1.ppt" /> <meta name="description" content="bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution" /> <meta name="generator" content="Drupal 7 (http://drupal.org)" /> <link rel="canonical" href="https://www.biorxiv.org/content/10.1101/078733v1" /> <link rel="shortlink" 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class="highwire-article-citation highwire-citation-type-highwire-article node21773" data-node-nid="21773" id="node-21773--21052423316" data-pisa="biorxiv;078733v1" data-pisa-master="biorxiv;078733" data-apath="/biorxiv/early/2016/10/01/078733.atom" data-hw-author-tooltip-instance="highwire_author_tooltip"><div class="highwire-cite highwire-cite-highwire-article highwire-citation-biorxiv-article-top clearfix has-author-tooltip" > <span class="biorxiv-article-type"> New Results </span> <h1 class="highwire-cite-title" id="page-title">Crystal structure and RNA-binding properties of an Hfq homolog from the deep-branching Aquificae: Conservation of the lateral RNA-binding mode</h1> <div class="highwire-cite-authors" ><span class="highwire-citation-authors"><span class="highwire-citation-author first" data-delta="0"><span class="nlm-given-names">Kimberly A</span> <span class="nlm-surname">Stanek</span></span>, <span class="highwire-citation-author" data-delta="1"><span class="nlm-given-names">Jennifer P</span> <span class="nlm-surname">West</span></span>, <span class="highwire-citation-author" data-delta="2"><span class="nlm-given-names">Peter S</span> <span class="nlm-surname">Randolph</span></span>, <span class="highwire-citation-author" data-delta="3"><span class="nlm-given-names">Cameron</span> <span class="nlm-surname">Mura</span></span></span></div> <div class="highwire-cite-metadata" ><span class="highwire-cite-metadata-doi highwire-cite-metadata"><span class="label">doi:</span> https://doi.org/10.1101/078733 </span></div> </div> <div id="hw-article-author-popups-node-21773--21052423316" style="display: none;"><div class="author-tooltip-0"><div class="author-tooltip-name">Kimberly A Stanek </div><div class="author-tooltip-affiliation"><span class="author-tooltip-text"><div class='author-affiliation'><span class='nlm-sup'>a</span><span class='nlm-institution'>Department of Chemistry, University of Virginia</span>, 409 McCormick Road, Charlottesville, VA, 22904, <span class='nlm-country'>USA</span></div></span></div><ul class="author-tooltip-find-more"><li class="author-tooltip-gs-link first"><a href="/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Kimberly%2BA%2BStanek%2B" target="_blank" class="" data-icon-position="" data-hide-link-title="0">Find this author on Google Scholar</a></li><li class="author-tooltip-pubmed-link"><a href="/lookup/external-ref?access_num=Stanek%20KA&link_type=AUTHORSEARCH" target="_blank" class="" data-icon-position="" data-hide-link-title="0">Find this author on PubMed</a></li><li class="author-site-search-link last"><a href="/search/author1%3AKimberly%2BA%2BStanek%2B" rel="nofollow" class="" data-icon-position="" data-hide-link-title="0">Search for this author on this site</a></li></ul></div><div class="author-tooltip-1"><div class="author-tooltip-name">Jennifer P West </div><div class="author-tooltip-affiliation"><span class="author-tooltip-text"><div class='author-affiliation'><span class='nlm-sup'>a</span><span class='nlm-institution'>Department of Chemistry, University of Virginia</span>, 409 McCormick Road, Charlottesville, VA, 22904, <span class='nlm-country'>USA</span></div></span></div><ul class="author-tooltip-find-more"><li class="author-tooltip-gs-link first"><a href="/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Jennifer%2BP%2BWest%2B" target="_blank" class="" data-icon-position="" data-hide-link-title="0">Find this author on Google Scholar</a></li><li class="author-tooltip-pubmed-link"><a href="/lookup/external-ref?access_num=West%20JP&link_type=AUTHORSEARCH" target="_blank" class="" data-icon-position="" data-hide-link-title="0">Find this author on PubMed</a></li><li class="author-site-search-link last"><a href="/search/author1%3AJennifer%2BP%2BWest%2B" rel="nofollow" class="" data-icon-position="" data-hide-link-title="0">Search for this author on this site</a></li></ul></div><div class="author-tooltip-2"><div class="author-tooltip-name">Peter S Randolph </div><div class="author-tooltip-affiliation"><span class="author-tooltip-text"><div class='author-affiliation'><span class='nlm-sup'>a</span><span class='nlm-institution'>Department of Chemistry, University of Virginia</span>, 409 McCormick Road, Charlottesville, VA, 22904, <span class='nlm-country'>USA</span></div></span></div><ul class="author-tooltip-find-more"><li class="author-tooltip-gs-link first"><a href="/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Peter%2BS%2BRandolph%2B" target="_blank" class="" data-icon-position="" data-hide-link-title="0">Find this author on Google Scholar</a></li><li class="author-tooltip-pubmed-link"><a href="/lookup/external-ref?access_num=Randolph%20PS&link_type=AUTHORSEARCH" target="_blank" class="" data-icon-position="" data-hide-link-title="0">Find this author on PubMed</a></li><li class="author-site-search-link last"><a href="/search/author1%3APeter%2BS%2BRandolph%2B" rel="nofollow" class="" data-icon-position="" data-hide-link-title="0">Search for this author on this site</a></li></ul></div><div class="author-tooltip-3"><div class="author-tooltip-name">Cameron Mura </div><div class="author-tooltip-affiliation"><span class="author-tooltip-text"><div class='author-affiliation'><span class='nlm-sup'>a</span><span class='nlm-institution'>Department of Chemistry, University of Virginia</span>, 409 McCormick Road, Charlottesville, VA, 22904, <span class='nlm-country'>USA</span></div></span></div><ul class="author-tooltip-find-more"><li class="author-tooltip-gs-link first"><a href="/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Cameron%2BMura%2B" target="_blank" class="" data-icon-position="" data-hide-link-title="0">Find this author on Google Scholar</a></li><li class="author-tooltip-pubmed-link"><a href="/lookup/external-ref?access_num=Mura%20C&link_type=AUTHORSEARCH" 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xmlns="http://www.w3.org/1999/xhtml" data-highwire-cite-ref-tooltip-instance="highwire_reflinks_tooltip" class="content-block-markup" xmlns:xhtml="http://www.w3.org/1999/xhtml"><div class="article abstract-view "><span class="highwire-journal-article-marker-start"></span><div class="section abstract" id="abstract-1"><h2>Abstract</h2><div id="sec-1" class="subsection"><p id="p-2"><strong>Synopsis</strong> The structure of an Hfq homolog from the deep-branching thermophilic bacterium <em>Aquifex aeolicus</em>, determined to 1.5-Å resolution both in <em>apo</em> form and bound to a uridine-rich RNA, reveals a conserved, pre-organized RNA-binding pocket on the lateral rim of the Hfq hexamer.</p></div><div id="sec-2" class="subsection"><p id="p-3"><strong>Abstract</strong> The host factor Hfq, as the bacterial branch of the Sm family, is an RNA-binding protein involved in post-transcriptional regulation of mRNA expression and turnover. Hfq facilitates pairing between small regulatory RNAs (sRNA) and their corresponding mRNA targets by binding both RNAs and bringing them into close proximity. Hfq homologs self-assemble into homo-hexameric rings, with at least two distinct surfaces that bind RNA. Recently, another binding site—dubbed the ‘lateral rim’—has been implicated in sRNA•mRNA annealing; the RNA-binding properties of this site appear to be rather subtle, and its degree of evolutionary conservation is unknown. An Hfq homolog has been identified in the phylogenetically deep-branching thermophile <em>Aquifex aeolicus</em> (<em>Aae</em>), but little is known about the structures and functions of Hfq from basal bacterial lineages such as the Aquificae. Thus, we have cloned, overexpressed, purified, crystallized, and biochemically characterized <em>Aae</em> Hfq. We have determined the structures of <em>Aae</em> Hfq in space-groups <em>P</em>1 and <em>P</em>6, both to 1.5 Å resolution, and we have discovered nanomolar-scale binding affinities for uridine- and adenosine-rich RNAs. Co-crystallization with U<sub>6</sub> RNA reveals that the outer rim of the <em>Aae</em> Hfq hexamer features a well-defined binding pocket that is selective for uracil. This <em>Aae</em> Hfq structure, combined with biochemical and biophysical characterization of the homolog, reveals deep evolutionary conservation of the lateral RNA-binding mode, and lays a foundation for further studies of Hfq-associated RNA biology in ancient bacterial phyla.</p></div></div><span class="highwire-journal-article-marker-end"></span></div><span class="related-urls"></span></div></div> </div> </div> <div class="panel-separator"></div><div class="panel-pane pane-biorxiv-copyright" > <div class="pane-content"> <div class="field field-name-field-highwire-copyright field-type-text field-label-inline clearfix"><div class="field-label">Copyright </div><div class="field-items"><div class="field-item even">The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.<span class="license-type-none"> All rights reserved. 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highwire-citation-biorxiv-article-pap-list clearfix" > <div class="highwire-cite-title" > <div class="highwire-cite-title">Crystal structure and RNA-binding properties of an Hfq homolog from the deep-branching Aquificae: Conservation of the lateral RNA-binding mode</div> </div> <div class="highwire-cite-authors" ><span class="highwire-citation-authors"><span class="highwire-citation-author first" data-delta="0"><span class="nlm-given-names">Kimberly A</span> <span class="nlm-surname">Stanek</span></span>, <span class="highwire-citation-author" data-delta="1"><span class="nlm-given-names">Jennifer P</span> <span class="nlm-surname">West</span></span>, <span class="highwire-citation-author" data-delta="2"><span class="nlm-given-names">Peter S</span> <span class="nlm-surname">Randolph</span></span>, <span class="highwire-citation-author" data-delta="3"><span class="nlm-given-names">Cameron</span> <span class="nlm-surname">Mura</span></span></span></div> <div class="highwire-cite-metadata" ><span class="highwire-cite-metadata-journal highwire-cite-metadata">bioRxiv </span><span class="highwire-cite-metadata-pages highwire-cite-metadata">078733; </span><span class="highwire-cite-metadata-doi highwire-cite-metadata"><span class="doi_label">doi:</span> https://doi.org/10.1101/078733 </span></div> </div> </div> </div> <div class="highwire-citation-formats"> <h2>Citation Manager Formats</h2> <div class="highwire-citation-formats-links"> <span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.spage&rft.epage&rft.atitle=Crystal%20structure%20and%20RNA-binding%20properties%20of%20an%20Hfq%20homolog%20from%20the%20deep-branching%20Aquificae%3A%20Conservation%20of%20the%20lateral%20RNA-binding%20mode&rft.volume&rft.issue&rft.date=2016-01-01%2000%3A00%3A00&rft.stitle&rft.jtitle=bioRxiv&rft.au=Stanek%2C+Kimberly+A&rft.au=West%2C+Jennifer+P&rft.au=Randolph%2C+Peter+S&rft.au=Mura%2C+Cameron"></span><ul class="hw-citation-links inline 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