Bacterial Group II Intron Genomic Neighborhoods Reflect Survival Strategies: Hiding and Hijacking
Abstract Group II (gII) introns are mobile retroelements that can spread to new DNA sites through retrotransposition, which can be influenced by a variety of host factors. To determine if these host factors bear any relationship to the genomic location of gII introns, we developed a bioinformatic pi...
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Veröffentlicht in: | Molecular biology and evolution 2020-07, Vol.37 (7), p.1942-1948 |
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container_issue | 7 |
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container_title | Molecular biology and evolution |
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creator | Waldern, Justin Schiraldi, Nicholas J Belfort, Marlene Novikova, Olga |
description | Abstract
Group II (gII) introns are mobile retroelements that can spread to new DNA sites through retrotransposition, which can be influenced by a variety of host factors. To determine if these host factors bear any relationship to the genomic location of gII introns, we developed a bioinformatic pipeline wherein we focused on the genomic neighborhoods of bacterial gII introns within their native contexts and sought to determine global relationships between introns and their surrounding genes. We found that, although gII introns inhabit diverse regions, these neighborhoods are often functionally enriched for genes that could promote gII intron retention or proliferation. On one hand, we observe that gII introns are frequently found hiding in mobile elements or after transcription terminators. On the other hand, gII introns are enriched in locations in which they could hijack host functions for their movement, potentially timing expression of the intron with genes that produce favorable conditions for retrotransposition. Thus, we propose that gII intron distributions have been shaped by relationships with their surrounding genomic neighbors. |
doi_str_mv | 10.1093/molbev/msaa055 |
format | Article |
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Group II (gII) introns are mobile retroelements that can spread to new DNA sites through retrotransposition, which can be influenced by a variety of host factors. To determine if these host factors bear any relationship to the genomic location of gII introns, we developed a bioinformatic pipeline wherein we focused on the genomic neighborhoods of bacterial gII introns within their native contexts and sought to determine global relationships between introns and their surrounding genes. We found that, although gII introns inhabit diverse regions, these neighborhoods are often functionally enriched for genes that could promote gII intron retention or proliferation. On one hand, we observe that gII introns are frequently found hiding in mobile elements or after transcription terminators. On the other hand, gII introns are enriched in locations in which they could hijack host functions for their movement, potentially timing expression of the intron with genes that produce favorable conditions for retrotransposition. Thus, we propose that gII intron distributions have been shaped by relationships with their surrounding genomic neighbors.</description><identifier>ISSN: 0737-4038</identifier><identifier>EISSN: 1537-1719</identifier><identifier>DOI: 10.1093/molbev/msaa055</identifier><identifier>PMID: 32134458</identifier><language>eng</language><publisher>United States: Oxford University Press</publisher><subject>Discoveries ; Genome, Bacterial ; Interspersed Repetitive Sequences ; Introns ; Replicon</subject><ispartof>Molecular biology and evolution, 2020-07, Vol.37 (7), p.1942-1948</ispartof><rights>The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. 2020</rights><rights>The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c424t-54b332f2a0c0ddef41fdb36e7795b8804f8cb2b35530bcba77cda0fee47f3b8f3</citedby><cites>FETCH-LOGICAL-c424t-54b332f2a0c0ddef41fdb36e7795b8804f8cb2b35530bcba77cda0fee47f3b8f3</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/PMC7306698/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7306698/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,885,1604,27924,27925,53791,53793</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/32134458$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Arkhipova, Irina</contributor><creatorcontrib>Waldern, Justin</creatorcontrib><creatorcontrib>Schiraldi, Nicholas J</creatorcontrib><creatorcontrib>Belfort, Marlene</creatorcontrib><creatorcontrib>Novikova, Olga</creatorcontrib><title>Bacterial Group II Intron Genomic Neighborhoods Reflect Survival Strategies: Hiding and Hijacking</title><title>Molecular biology and evolution</title><addtitle>Mol Biol Evol</addtitle><description>Abstract
Group II (gII) introns are mobile retroelements that can spread to new DNA sites through retrotransposition, which can be influenced by a variety of host factors. To determine if these host factors bear any relationship to the genomic location of gII introns, we developed a bioinformatic pipeline wherein we focused on the genomic neighborhoods of bacterial gII introns within their native contexts and sought to determine global relationships between introns and their surrounding genes. We found that, although gII introns inhabit diverse regions, these neighborhoods are often functionally enriched for genes that could promote gII intron retention or proliferation. On one hand, we observe that gII introns are frequently found hiding in mobile elements or after transcription terminators. On the other hand, gII introns are enriched in locations in which they could hijack host functions for their movement, potentially timing expression of the intron with genes that produce favorable conditions for retrotransposition. Thus, we propose that gII intron distributions have been shaped by relationships with their surrounding genomic neighbors.</description><subject>Discoveries</subject><subject>Genome, Bacterial</subject><subject>Interspersed Repetitive Sequences</subject><subject>Introns</subject><subject>Replicon</subject><issn>0737-4038</issn><issn>1537-1719</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2020</creationdate><recordtype>article</recordtype><sourceid>TOX</sourceid><sourceid>EIF</sourceid><recordid>eNqFkcFPHCEUh4nR6Fa9emw46mEVBhhmPJioaddNjCbangkwj13szLDCzCb-99LsatqTJx553_vBy4fQCSXnlNTsogutgfVFl7QmQuygCRVMTqmk9S6aEJlrTlh1gL6l9EII5bws99EBKyjjXFQTpG-0HSB63eJZDOMKz-d43g8x9HgGfei8xQ_gF0sT4jKEJuEncC3YAT-Pce3Xeex5iHqAhYd0ie984_sF1n2Tyxdt_-TbEdpzuk1wvD0P0e-fP37d3k3vH2fz2-v7qeUFH6aCG8YKV2hiSdOA49Q1hpUgZS1MVRHuKmsKw4RgxFijpbSNJg6AS8dM5dghutrkrkbTQWMhb6FbtYq-0_FNBe3V_53eL9UirJVkpCzrKgecbgNieB0hDarzyULb6h7CmFTBJK1EyWqe0fMNamNIKYL7fIYS9deL2nhRWy954Pu_n_vEP0Rk4GwDZAdfhb0DKpmcvA</recordid><startdate>20200701</startdate><enddate>20200701</enddate><creator>Waldern, Justin</creator><creator>Schiraldi, Nicholas J</creator><creator>Belfort, Marlene</creator><creator>Novikova, Olga</creator><general>Oxford University Press</general><scope>TOX</scope><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>7X8</scope><scope>5PM</scope></search><sort><creationdate>20200701</creationdate><title>Bacterial Group II Intron Genomic Neighborhoods Reflect Survival Strategies: Hiding and Hijacking</title><author>Waldern, Justin ; Schiraldi, Nicholas J ; Belfort, Marlene ; Novikova, Olga</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c424t-54b332f2a0c0ddef41fdb36e7795b8804f8cb2b35530bcba77cda0fee47f3b8f3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2020</creationdate><topic>Discoveries</topic><topic>Genome, Bacterial</topic><topic>Interspersed Repetitive Sequences</topic><topic>Introns</topic><topic>Replicon</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Waldern, Justin</creatorcontrib><creatorcontrib>Schiraldi, Nicholas J</creatorcontrib><creatorcontrib>Belfort, Marlene</creatorcontrib><creatorcontrib>Novikova, Olga</creatorcontrib><collection>Oxford Journals Open Access Collection</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Molecular biology and evolution</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Waldern, Justin</au><au>Schiraldi, Nicholas J</au><au>Belfort, Marlene</au><au>Novikova, Olga</au><au>Arkhipova, Irina</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Bacterial Group II Intron Genomic Neighborhoods Reflect Survival Strategies: Hiding and Hijacking</atitle><jtitle>Molecular biology and evolution</jtitle><addtitle>Mol Biol Evol</addtitle><date>2020-07-01</date><risdate>2020</risdate><volume>37</volume><issue>7</issue><spage>1942</spage><epage>1948</epage><pages>1942-1948</pages><issn>0737-4038</issn><eissn>1537-1719</eissn><abstract>Abstract
Group II (gII) introns are mobile retroelements that can spread to new DNA sites through retrotransposition, which can be influenced by a variety of host factors. To determine if these host factors bear any relationship to the genomic location of gII introns, we developed a bioinformatic pipeline wherein we focused on the genomic neighborhoods of bacterial gII introns within their native contexts and sought to determine global relationships between introns and their surrounding genes. We found that, although gII introns inhabit diverse regions, these neighborhoods are often functionally enriched for genes that could promote gII intron retention or proliferation. On one hand, we observe that gII introns are frequently found hiding in mobile elements or after transcription terminators. On the other hand, gII introns are enriched in locations in which they could hijack host functions for their movement, potentially timing expression of the intron with genes that produce favorable conditions for retrotransposition. Thus, we propose that gII intron distributions have been shaped by relationships with their surrounding genomic neighbors.</abstract><cop>United States</cop><pub>Oxford University Press</pub><pmid>32134458</pmid><doi>10.1093/molbev/msaa055</doi><tpages>7</tpages><oa>free_for_read</oa></addata></record> |
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subjects | Discoveries Genome, Bacterial Interspersed Repetitive Sequences Introns Replicon |
title | Bacterial Group II Intron Genomic Neighborhoods Reflect Survival Strategies: Hiding and Hijacking |
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