Why so narrow: Distribution of anti-sense regulated, type I toxin-antitoxin systems compared with type II and type III systems
Toxin-antitoxin (TA) systems are gene modules that appear to be horizontally mobile across a wide range of prokaryotes. It has been proposed that type I TA systems, with an antisense RNA-antitoxin, are less mobile than other TAs that rely on direct toxin-antitoxin binding but no direct comparisons h...
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| Veröffentlicht in: | RNA biology 2017-03, Vol.14 (3), p.275-280 |
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| creator | Coray, Dorien S. Wheeler, Nicole E. Heinemann, Jack A. Gardner, Paul P. |
| description | Toxin-antitoxin (TA) systems are gene modules that appear to be horizontally mobile across a wide range of prokaryotes. It has been proposed that type I TA systems, with an antisense RNA-antitoxin, are less mobile than other TAs that rely on direct toxin-antitoxin binding but no direct comparisons have been made. We searched for type I, II and III toxin families using iterative searches with profile hidden Markov models across phyla and replicons. The distribution of type I toxin families were comparatively narrow, but these patterns weakened with recently discovered families. We discuss how the function and phenotypes of TA systems as well as biases in our search methods may account for differences in their distribution. |
| doi_str_mv | 10.1080/15476286.2016.1272747 |
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It has been proposed that type I TA systems, with an antisense RNA-antitoxin, are less mobile than other TAs that rely on direct toxin-antitoxin binding but no direct comparisons have been made. We searched for type I, II and III toxin families using iterative searches with profile hidden Markov models across phyla and replicons. The distribution of type I toxin families were comparatively narrow, but these patterns weakened with recently discovered families. We discuss how the function and phenotypes of TA systems as well as biases in our search methods may account for differences in their distribution.</description><identifier>ISSN: 1547-6286</identifier><identifier>ISSN: 1555-8584</identifier><identifier>EISSN: 1555-8584</identifier><identifier>DOI: 10.1080/15476286.2016.1272747</identifier><identifier>PMID: 28067598</identifier><language>eng</language><publisher>United States: Taylor & Francis</publisher><subject>Antisense RNA ; Antitoxins - genetics ; Bacterial Toxins - genetics ; Databases, Genetic ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; genes ; horizontal gene transfer ; Interspersed Repetitive Sequences ; Letter to the Editor ; Multigene Family ; Operon ; Phylogeny ; post-segregational killing ; prokaryotic cells ; RNA ; RNA, Antisense - genetics ; toxin-antitoxin systems ; toxins</subject><ispartof>RNA biology, 2017-03, Vol.14 (3), p.275-280</ispartof><rights>Published with license by Taylor & Francis Group, LLC © Dorien S. Coray, Nicole E. Wheeler, Jack A. Heinemann, and Paul P. Gardner.</rights><rights>2017 The Author(s). 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We discuss how the function and phenotypes of TA systems as well as biases in our search methods may account for differences in their distribution.</description><subject>Antisense RNA</subject><subject>Antitoxins - genetics</subject><subject>Bacterial Toxins - genetics</subject><subject>Databases, Genetic</subject><subject>Gene Expression Regulation, Bacterial</subject><subject>Gene Transfer, Horizontal</subject><subject>genes</subject><subject>horizontal gene transfer</subject><subject>Interspersed Repetitive Sequences</subject><subject>Letter to the Editor</subject><subject>Multigene Family</subject><subject>Operon</subject><subject>Phylogeny</subject><subject>post-segregational killing</subject><subject>prokaryotic cells</subject><subject>RNA</subject><subject>RNA, Antisense - genetics</subject><subject>toxin-antitoxin systems</subject><subject>toxins</subject><issn>1547-6286</issn><issn>1555-8584</issn><issn>1555-8584</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2017</creationdate><recordtype>article</recordtype><sourceid>0YH</sourceid><sourceid>EIF</sourceid><recordid>eNqFkUmP0zAYhiMEYhb4CSAfOZDi3Q4HBJphqTQSFxBHy_UyNUrsYjuUXPjtJLQdwQVOfiU_3-vlaZonCK4QlPAFYlRwLPkKQ8RXCAssqLjXnCPGWCuZpPeXTEW7QGfNRSlfISRcduxhc4Yl5IJ18rz5-WU7gZJA1Dmn_UtwHUrNYTPWkCJIHuhYQ1tcLA5kdzv2ujr7HNRp58Aa1PQjxHZBfidQplLdUIBJw05nZ8E-1O0RXs9V9pTXJ_RR88DrvrjHx_Wy-fzu7aerD-3Nx_frqzc3rWEQ1VY7TgRBrOPEY7iBUjqmiTcCUUGpEwxrI4THSHBLjCUUQo29N4Z3lBJryWXz6tC7GzeDs8bFmnWvdjkMOk8q6aD-3olhq27Td8UIF5jhueDZsSCnb6MrVQ2hGNf3Oro0FoUZQx2Z_5r9F0WScck5IWhG2QE1OZWSnb-7EYJq0axOmtWiWR01z3NP_3zO3dTJ6wy8PgAh-pQHvU-5t6rqqU_ZZx1NKIr8-4xfVl-5CA</recordid><startdate>20170304</startdate><enddate>20170304</enddate><creator>Coray, Dorien S.</creator><creator>Wheeler, Nicole E.</creator><creator>Heinemann, Jack A.</creator><creator>Gardner, Paul P.</creator><general>Taylor & Francis</general><scope>0YH</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>7S9</scope><scope>L.6</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0003-4599-9164</orcidid></search><sort><creationdate>20170304</creationdate><title>Why so narrow: Distribution of anti-sense regulated, type I toxin-antitoxin systems compared with type II and type III systems</title><author>Coray, Dorien S. ; Wheeler, Nicole E. ; Heinemann, Jack A. ; Gardner, Paul P.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c501t-ae637315963f20b088e5a3fc714744e752ac77f2176d3cd3400a2ffcc69443dd3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2017</creationdate><topic>Antisense RNA</topic><topic>Antitoxins - genetics</topic><topic>Bacterial Toxins - genetics</topic><topic>Databases, Genetic</topic><topic>Gene Expression Regulation, Bacterial</topic><topic>Gene Transfer, Horizontal</topic><topic>genes</topic><topic>horizontal gene transfer</topic><topic>Interspersed Repetitive Sequences</topic><topic>Letter to the Editor</topic><topic>Multigene Family</topic><topic>Operon</topic><topic>Phylogeny</topic><topic>post-segregational killing</topic><topic>prokaryotic cells</topic><topic>RNA</topic><topic>RNA, Antisense - genetics</topic><topic>toxin-antitoxin systems</topic><topic>toxins</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Coray, Dorien S.</creatorcontrib><creatorcontrib>Wheeler, Nicole E.</creatorcontrib><creatorcontrib>Heinemann, Jack A.</creatorcontrib><creatorcontrib>Gardner, Paul P.</creatorcontrib><collection>Taylor & Francis Open Access</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>AGRICOLA</collection><collection>AGRICOLA - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>RNA biology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Coray, Dorien S.</au><au>Wheeler, Nicole E.</au><au>Heinemann, Jack A.</au><au>Gardner, Paul P.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Why so narrow: Distribution of anti-sense regulated, type I toxin-antitoxin systems compared with type II and type III systems</atitle><jtitle>RNA biology</jtitle><addtitle>RNA Biol</addtitle><date>2017-03-04</date><risdate>2017</risdate><volume>14</volume><issue>3</issue><spage>275</spage><epage>280</epage><pages>275-280</pages><issn>1547-6286</issn><issn>1555-8584</issn><eissn>1555-8584</eissn><abstract>Toxin-antitoxin (TA) systems are gene modules that appear to be horizontally mobile across a wide range of prokaryotes. It has been proposed that type I TA systems, with an antisense RNA-antitoxin, are less mobile than other TAs that rely on direct toxin-antitoxin binding but no direct comparisons have been made. We searched for type I, II and III toxin families using iterative searches with profile hidden Markov models across phyla and replicons. The distribution of type I toxin families were comparatively narrow, but these patterns weakened with recently discovered families. We discuss how the function and phenotypes of TA systems as well as biases in our search methods may account for differences in their distribution.</abstract><cop>United States</cop><pub>Taylor & Francis</pub><pmid>28067598</pmid><doi>10.1080/15476286.2016.1272747</doi><tpages>6</tpages><orcidid>https://orcid.org/0000-0003-4599-9164</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | Antisense RNA Antitoxins - genetics Bacterial Toxins - genetics Databases, Genetic Gene Expression Regulation, Bacterial Gene Transfer, Horizontal genes horizontal gene transfer Interspersed Repetitive Sequences Letter to the Editor Multigene Family Operon Phylogeny post-segregational killing prokaryotic cells RNA RNA, Antisense - genetics toxin-antitoxin systems toxins |
| title | Why so narrow: Distribution of anti-sense regulated, type I toxin-antitoxin systems compared with type II and type III systems |
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