<br><div> <head profile="http://www.w3.org/1999/xhtml/vocab"> <!--[if IE]><![endif]--> <meta http-equiv="Content-Type" content="text/html; charset=utf-8"/> <link rel="dns-prefetch" href="//scholar.google.com"/> <link rel="dns-prefetch" href="//pnas-movie.glencoesoftware.com"/> <link rel="dns-prefetch" href="//www.google.com"/> <link rel="dns-prefetch" href="//www.google-analytics.com"/> <link rel="dns-prefetch" href="//stats.g.doubleclick.net"/> <meta name="viewport" content="initial-scale=1, maximum-scale=1, width=device-width, user-scalable=yes"/> <link rel="shortcut icon" href="https://www.pnas.org/sites/default/files/images/favicon.ico" type="image/vnd.microsoft.icon"/> <link rel="canonical" href="https://www.pnas.org/content/early/2020/07/15/2001888117"/> <meta name="Generator" content="Drupal 7 (http://drupal.org)"/> <link rel="alternate" type="application/pdf" title="Full Text (PDF)" href="http://www.pnas.org/content/early/2020/07/15/2001888117.full.pdf"/> <link rel="alternate" type="text/plain" title="Full Text (Plain)" href="http://www.pnas.org/content/early/2020/07/15/2001888117.full.txt"/> <link rel="alternate" type="application/vnd.ms-powerpoint" title="Powerpoint" href="http://www.pnas.org/content/early/2020/07/15/2001888117.ppt"/> <meta name="citation_funding_source" content="citation_grant_number=n/a;"/> <meta name="type" content="article"/> <meta name="category" content="research-article"/> <meta name="HW.identifier" content="/pnas/early/2020/07/15/2001888117.atom"/> <meta name="HW.pisa" content="pnas;2001888117v1"/> <meta name="DC.Format" content="text/html"/> <meta name="DC.Language" content="en"/> <meta name="DC.Title" content="High-throughput discovery of phage receptors using transposon insertion sequencing of bacteria"/> <meta name="DC.Identifier" content="10.1073/pnas.2001888117"/> <meta name="DC.Date" content="2020-07-16"/> <meta name="DC.Publisher" content="National Academy of Sciences"/> <meta name="DC.Rights" content="Copyright © 2020 the Author(s). Published by PNAS.. https://creativecommons.org/licenses/by-nc-nd/4.0/This open access article is distributed under Creative Commons Attribution-NonCommercial-NoDerivatives License 4.0 (CC BY-NC-ND)."/> <meta name="DC.AccessRights" content="open-access"/> <meta name="DC.Description" content="Bacteriophages (phages), viruses that infect bacteria, are the most abundant microbes on Earth. Extreme specificity to host species or even strains of bacteria makes phages amenable to particular biotechnical applications. This specificity is partially governed by the surface-expressed structures of bacteria that phages use as cell-binding receptors. However, these receptors remain less-studied in phage biology, because their discovery relies on laborious methods utilizing well-characterized bacteria. Here we present INSeq screens as a rapid, high-throughput tool to identify candidate phage receptors. This method was successful in identifying receptors for previously well-characterized phages T2, T4, T6, and T7 as well as identifying receptors for newly isolated phages R3, U115, EC14, EC35, and 8S. As the most abundant microbes on Earth, novel bacteriophages (phages; bacteria-specific viruses) are readily isolated from environmental samples. However, it remains challenging to characterize phage–bacteria interactions, such as the host receptor(s) phages bind to initiate infection. Here, we tested whether transposon insertion sequencing (INSeq) could be used to identify bacterial genes involved in phage binding. As proof of concept, results showed that INSeq screens successfully identified genes encoding known receptors for previously characterized viruses of Escherichia coli (phages T6, T2, T4, and T7). INSeq screens were then used to identify genes involved during infection of six newly isolated coliphages. Results showed that candidate receptors could be successfully identified for the majority (five of six) of the phages; furthermore, genes encoding the phage receptor(s) were the top hit(s) in the analyses of the successful screens. INSeq screens provide a generally useful method for high-throughput discovery of phage receptors. We discuss limitations of our approach when examining uncharacterized phages, as well as usefulness of the method for exploring the evolution of broad versus narrow use of cellular receptors among phages in the biosphere."/> <meta name="DC.Contributor" content="Kaitlyn E. Kortright"/> <meta name="DC.Contributor" content="Benjamin K. Chan"/> <meta name="DC.Contributor" content="Paul E. Turner"/> <meta name="article:published_time" content="2020-07-16"/> <meta name="article:section" content="Biological Sciences"/> <meta name="citation_title" content="High-throughput discovery of phage receptors using transposon insertion sequencing of bacteria"/> <meta name="citation_abstract" lang="en" content="<p>As the most abundant microbes on Earth, novel bacteriophages (phages; bacteria-specific viruses) are readily isolated from environmental samples. However, it remains challenging to characterize phage–bacteria interactions, such as the host receptor(s) phages bind to initiate infection. Here, we tested whether transposon insertion sequencing (INSeq) could be used to identify bacterial genes involved in phage binding. As proof of concept, results showed that INSeq screens successfully identified genes encoding known receptors for previously characterized viruses of <i>Escherichia coli</i> (phages T6, T2, T4, and T7). INSeq screens were then used to identify genes involved during infection of six newly isolated coliphages. Results showed that candidate receptors could be successfully identified for the majority (five of six) of the phages; furthermore, genes encoding the phage receptor(s) were the top hit(s) in the analyses of the successful screens. INSeq screens provide a generally useful method for high-throughput discovery of phage receptors. We discuss limitations of our approach when examining uncharacterized phages, as well as usefulness of the method for exploring the evolution of broad versus narrow use of cellular receptors among phages in the biosphere.</p>"/> <meta name="citation_abstract" lang="en" scheme="executive-summary" content="<h3>Significance</h3> <p>Bacteriophages (phages), viruses that infect bacteria, are the most abundant microbes on Earth. Extreme specificity to host species or even strains of bacteria makes phages amenable to particular biotechnical applications. This specificity is partially governed by the surface-expressed structures of bacteria that phages use as cell-binding receptors. However, these receptors remain less-studied in phage biology, because their discovery relies on laborious methods utilizing well-characterized bacteria. Here we present INSeq screens as a rapid, high-throughput tool to identify candidate phage receptors. This method was successful in identifying receptors for previously well-characterized phages T2, T4, T6, and T7 as well as identifying receptors for newly isolated phages R3, U115, EC14, EC35, and 8S.</p>"/> <meta name="citation_journal_title" content="Proceedings of the National Academy of Sciences"/> <meta name="citation_publisher" content="National Academy of Sciences"/> <meta name="citation_publication_date" content="2020/07/16"/> <meta name="citation_mjid" content="pnas;2001888117v1"/> <meta name="citation_id" content="2001888117v1"/> <meta name="citation_public_url" content="https://www.pnas.org/content/early/2020/07/15/2001888117"/> <meta name="citation_abstract_html_url" content="https://www.pnas.org/content/early/2020/07/15/2001888117.abstract"/> <meta name="citation_full_html_url" content="https://www.pnas.org/content/early/2020/07/15/2001888117.full"/> <meta name="citation_pdf_url" content="https://www.pnas.org/content/pnas/early/2020/07/15/2001888117.full.pdf"/> <meta name="citation_issn" content="0027-8424"/> <meta name="citation_issn" content="1091-6490"/> <meta name="citation_journal_abbrev" content="PNAS"/> <meta name="citation_doi" content="10.1073/pnas.2001888117"/> <meta name="citation_pmid" content="32675236"/> <meta name="citation_num_pages" content="10"/> <meta name="citation_article_type" content="Research Article"/> <meta name="citation_section" content="Biological Sciences"/> <meta name="citation_access" content="all"/> <meta name="citation_author" content="Kaitlyn E. 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Kazmierczak;citation_title=A screen for antibiotic resistance determinants reveals a fitness cost of the flagellum in Pseudomonas aeruginosa;citation_pages=e00682-19;citation_volume=202;citation_year=2020"/> <meta name="citation_reference" content="citation_journal_abbrev=Nat Methods;citation_author=B. Langmead;citation_author=S. L. Salzberg;citation_title=Fast gapped-read alignment with Bowtie 2.;citation_pages=357-359;citation_volume=9;citation_year=2012;citation_issue=4;citation_pmid=22388286;citation_doi=10.1038/nmeth.1923"/> <meta name="citation_reference" content="citation_title=Bacteriophages;citation_pages=151-155;citation_year=2009"/> <meta name="citation_fulltext_world_readable" content=""/> <meta name="twitter:title" content="High-throughput discovery of phage receptors using transposon insertion sequencing of bacteria"/> <meta name="twitter:card" content="summary_large_image"/> <meta name="twitter:image" content="https://www.pnas.org/content/early/2020/07/15/2001888117/F1.large.jpg"/> <meta name="twitter:description" content="Bacteriophages (phages), viruses that infect bacteria, are the most abundant microbes on Earth. Extreme specificity to host species or even strains of bacteria makes phages amenable to particular biotechnical applications. This specificity is partially governed by the surface-expressed structures of bacteria that phages use as cell-binding receptors. However, these receptors remain less-studied in phage biology, because their discovery relies on laborious methods utilizing well-characterized bacteria. Here we present INSeq screens as a rapid, high-throughput tool to identify candidate phage receptors. This method was successful in identifying receptors for previously well-characterized phages T2, T4, T6, and T7 as well as identifying receptors for newly isolated phages R3, U115, EC14, EC35, and 8S. As the most abundant microbes on Earth, novel bacteriophages (phages; bacteria-specific viruses) are readily isolated from environmental samples. However, it remains challenging to characterize phage–bacteria interactions, such as the host receptor(s) phages bind to initiate infection. Here, we tested whether transposon insertion sequencing (INSeq) could be used to identify bacterial genes involved in phage binding. As proof of concept, results showed that INSeq screens successfully identified genes encoding known receptors for previously characterized viruses of Escherichia coli (phages T6, T2, T4, and T7). INSeq screens were then used to identify genes involved during infection of six newly isolated coliphages. Results showed that candidate receptors could be successfully identified for the majority (five of six) of the phages; furthermore, genes encoding the phage receptor(s) were the top hit(s) in the analyses of the successful screens. INSeq screens provide a generally useful method for high-throughput discovery of phage receptors. We discuss limitations of our approach when examining uncharacterized phages, as well as usefulness of the method for exploring the evolution of broad versus narrow use of cellular receptors among phages in the biosphere."/> <meta name="og-title" property="og:title" content="High-throughput discovery of phage receptors using transposon insertion sequencing of bacteria"/> <meta name="og-url" property="og:url" content="https://www.pnas.org/content/early/2020/07/15/2001888117"/> <meta name="og-site-name" property="og:site_name" content="PNAS"/> <meta name="og-description" property="og:description" content="Bacteriophages (phages), viruses that infect bacteria, are the most abundant microbes on Earth. Extreme specificity to host species or even strains of bacteria makes phages amenable to particular biotechnical applications. This specificity is partially governed by the surface-expressed structures of bacteria that phages use as cell-binding receptors. However, these receptors remain less-studied in phage biology, because their discovery relies on laborious methods utilizing well-characterized bacteria. Here we present INSeq screens as a rapid, high-throughput tool to identify candidate phage receptors. This method was successful in identifying receptors for previously well-characterized phages T2, T4, T6, and T7 as well as identifying receptors for newly isolated phages R3, U115, EC14, EC35, and 8S. As the most abundant microbes on Earth, novel bacteriophages (phages; bacteria-specific viruses) are readily isolated from environmental samples. However, it remains challenging to characterize phage–bacteria interactions, such as the host receptor(s) phages bind to initiate infection. Here, we tested whether transposon insertion sequencing (INSeq) could be used to identify bacterial genes involved in phage binding. As proof of concept, results showed that INSeq screens successfully identified genes encoding known receptors for previously characterized viruses of Escherichia coli (phages T6, T2, T4, and T7). INSeq screens were then used to identify genes involved during infection of six newly isolated coliphages. Results showed that candidate receptors could be successfully identified for the majority (five of six) of the phages; furthermore, genes encoding the phage receptor(s) were the top hit(s) in the analyses of the successful screens. INSeq screens provide a generally useful method for high-throughput discovery of phage receptors. We discuss limitations of our approach when examining uncharacterized phages, as well as usefulness of the method for exploring the evolution of broad versus narrow use of cellular receptors among phages in the biosphere."/> <meta name="og-type" property="og:type" content="article"/> <meta name="og-image" property="og:image" content="https://www.pnas.org/content/early/2020/07/15/2001888117/F1.large.jpg"/> <meta name="format-detection" content="telephone=no"/> <title>High-throughput discovery of phage receptors using transposon insertion sequencing of bacteria | PNAS</title> <link type="text/css" rel="stylesheet" href="https://www.pnas.org/sites/default/files/advagg_css/css__zUOsaJT2-txr78Pro2jqp5HkKYs7CY9FbkfBemQXYlw__kiQOVz2drquY4Y9F8gINaFiOXWD3R3YCpizYXeeITSI__Jsi9FELnOGd8Izl-cQZlaPD8YovR4Sb_o7kms4MEc0E.css" media="all"/> <link type="text/css" rel="stylesheet" href="https://www.pnas.org/sites/all/modules/highwire/highwire/highwire.style.highwire.css?qdo5w1" media="all"/> <link type="text/css" rel="stylesheet" href="https://www.pnas.org/sites/default/files/advagg_css/css__IBZ9mHpn46TRp2BimuZ9LV8gzg5ve38Vt8Ur3OYiiIE__NtZxs4y1UkEH1BmzA2899OuPWrL4Vyfw35jNwF7gpGQ__Jsi9FELnOGd8Izl-cQZlaPD8YovR4Sb_o7kms4MEc0E.css" media="all"/> <link type="text/css" rel="stylesheet" href="//cdn.jsdelivr.net/qtip2/2.2.1/jquery.qtip.min.css" media="all"/> <link type="text/css" rel="stylesheet" href="https://www.pnas.org/sites/default/files/advagg_css/css__22ZTiNg-l1Oh3N_2YNTtQtEIQm3aRzbkzzzbjY2p8xQ__X6SoMpUVch0hUZhU5GhhA43N8gkW5jGOyL-zhqU413o__Jsi9FELnOGd8Izl-cQZlaPD8YovR4Sb_o7kms4MEc0E.css" media="all"/> <link type="text/css" rel="stylesheet" href="//pnas-movie.glencoesoftware.com/static/video-js.min.css" media="all"/> <link type="text/css" rel="stylesheet" href="https://www.pnas.org/sites/default/files/advagg_css/css__7CYEtfDxMu3CEBZ53TQrEfMpO7duR_XdIuTLye9W7Cc__CzzPXev2zJRWVry4kyDAKuuERTizWaGzrN8gCp2auaE__Jsi9FELnOGd8Izl-cQZlaPD8YovR4Sb_o7kms4MEc0E.css" media="all"/> <link type="text/css" rel="stylesheet" href="https://www.pnas.org/sites/default/files/advagg_css/css__SFa0RaACUzIjJkHcYBtVK313lbEjuTFPdV1LDKDJEjo__jXPoluCdY9OJ1bes_FwCXcdI2BYpoO-G9OnF0StiEQA__Jsi9FELnOGd8Izl-cQZlaPD8YovR4Sb_o7kms4MEc0E.css" media="all"/> <!--[if lt IE 9]><![endif]--> <!--[if lt IE 10]><![endif]--> </head> <body id="wp_automatic_ReadabilityBody"> <!-- Google Tag Manager --> <noscript><iframe src="http://www.googletagmanager.com/ns.html?id=GTM-NDVQMQ4" height="0" width="0" style="display:none;visibility:hidden"></iframe></noscript> <!-- End Google Tag Manager --> <div class="page" id="page"> <!-- /.section-header --> <section role="main" class="section section-content" id="section-content"> <div class="container-fluid zone-wrapper zone-content-wrapper"> <div class="zone zone-content row"> <div class="region region-content col-narrow-22 col-narrow-offset-1"> <div id="block-panels-mini-whats-new-in" class="block block-panels-mini"> <div class="content"> <div class="panel-display panel-1col clearfix" id="mini-panel-whats_new_in"> <div class="panel-panel panel-col"> <div> <div class="panel-pane pane-snippet pane-pnas-physical-sciences wni-dropdown"> <h3 class="pane-title"><span class="pane-title-text">Physical Sciences</span></h3> <div class="pane-content"> <div class="pnas-physical-sciences" id="pnas-physical-sciences"> <div class="snippet-content"> <h4>Featured Portals</h4> <h4>Articles by Topic</h4> </div> </div> </div> </div> <div class="panel-pane pane-snippet pane-pnas-social-sciences wni-dropdown"> <h3 class="pane-title"><span class="pane-title-text">Social Sciences</span></h3> <div class="pane-content"> <div class="pnas-social-sciences" id="pnas-social-sciences"> <div class="snippet-content"> <h4>Featured Portals</h4> <h4>Articles by Topic</h4> </div> </div> </div> </div> <div class="panel-pane pane-snippet pane-pnas-biological-sciences wni-dropdown"> <h3 class="pane-title"><span class="pane-title-text">Biological Sciences</span></h3> <div class="pane-content"> <div class="pnas-biological-sciences" id="pnas-biological-sciences"> <div class="snippet-content"> <h4>Featured Portals</h4> <h4>Articles by Topic</h4> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div><!-- /.zone-content --> </div><!-- /.zone-content-wrapper --> </section> <!-- /.section-content --> <!-- /.section-footer --> </div> <!-- /.page --> </body> </div>