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Recognition of core binding sites by bacteriophage integrases
Bacteriophage integrases promote recombination between DNA molecules that carry attachment sites. They are members of a large and widely distributed family of site-specific recombinases with diverse biological roles. The integrases of phages λ and HK022 are closely related members of this family, bu...
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Published in: | Journal of molecular biology 1998-04, Vol.277 (5), p.1059-1070 |
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description | Bacteriophage integrases promote recombination between DNA molecules that carry attachment sites. They are members of a large and widely distributed family of site-specific recombinases with diverse biological roles. The integrases of phages λ and HK022 are closely related members of this family, but neither protein efficiently recombines the attachment sites of the other phage. The nucleotides responsible for this specificity difference are located close to the points of recombinational strand exchange, within an integrase binding motif called the extended core binding site. There are four imperfectly repeated copies of this motif in each set of phage attachment sites, but only two, B′ and C, contain major specificity determinants. When these specificity determinants were replaced by the corresponding nucleotides from a site with the alternative specificity, the resulting mutant was recombined by both integrases. Thus, the determinants act by impeding recombination promoted by the non-cognate integrase. We found that identical nucleotide substitutions within different core site copies had different effects on recombination, suggesting that integrase does not recognize each of the extended core binding sites in the same way. Finally, substitution at several positions in λ integrase with the corresponding HK022-specific amino acids prevents recombination of λ attachment sites, and this defect can be suppressed in an allele-specific manner by appropriate substitutions of HK022-specific nucleotides in the extended core binding sites. |
doi_str_mv | 10.1006/jmbi.1998.1642 |
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They are members of a large and widely distributed family of site-specific recombinases with diverse biological roles. The integrases of phages λ and HK022 are closely related members of this family, but neither protein efficiently recombines the attachment sites of the other phage. The nucleotides responsible for this specificity difference are located close to the points of recombinational strand exchange, within an integrase binding motif called the extended core binding site. There are four imperfectly repeated copies of this motif in each set of phage attachment sites, but only two, B′ and C, contain major specificity determinants. When these specificity determinants were replaced by the corresponding nucleotides from a site with the alternative specificity, the resulting mutant was recombined by both integrases. Thus, the determinants act by impeding recombination promoted by the non-cognate integrase. We found that identical nucleotide substitutions within different core site copies had different effects on recombination, suggesting that integrase does not recognize each of the extended core binding sites in the same way. Finally, substitution at several positions in λ integrase with the corresponding HK022-specific amino acids prevents recombination of λ attachment sites, and this defect can be suppressed in an allele-specific manner by appropriate substitutions of HK022-specific nucleotides in the extended core binding sites.</description><identifier>ISSN: 0022-2836</identifier><identifier>EISSN: 1089-8638</identifier><identifier>DOI: 10.1006/jmbi.1998.1642</identifier><identifier>PMID: 9571022</identifier><language>eng</language><publisher>England: Elsevier Ltd</publisher><subject>Amino Acid Sequence ; Bacteriophages - enzymology ; Binding Sites - genetics ; Coliphages - enzymology ; DNA-protein interaction ; evolution ; Integrases - chemistry ; Integrases - genetics ; lysogeny ; Molecular Sequence Data ; Mutagenesis - genetics ; Plasmids - genetics ; Recombination, Genetic - genetics ; Sequence Alignment ; site-specific recombination ; specificity determinants ; Viral Proteins - metabolism</subject><ispartof>Journal of molecular biology, 1998-04, Vol.277 (5), p.1059-1070</ispartof><rights>1998 Academic Press</rights><rights>Copyright 1998 Academic Press Limited.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c370t-e0fd1d6a4b92801f54390721e940340a30afb5f9dffaebe807573d7af82537af3</citedby><cites>FETCH-LOGICAL-c370t-e0fd1d6a4b92801f54390721e940340a30afb5f9dffaebe807573d7af82537af3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,780,784,27924,27925</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/9571022$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Dorgai, László</creatorcontrib><creatorcontrib>Sloan, Sieghild</creatorcontrib><creatorcontrib>Weisberg, Robert A</creatorcontrib><title>Recognition of core binding sites by bacteriophage integrases</title><title>Journal of molecular biology</title><addtitle>J Mol Biol</addtitle><description>Bacteriophage integrases promote recombination between DNA molecules that carry attachment sites. They are members of a large and widely distributed family of site-specific recombinases with diverse biological roles. The integrases of phages λ and HK022 are closely related members of this family, but neither protein efficiently recombines the attachment sites of the other phage. The nucleotides responsible for this specificity difference are located close to the points of recombinational strand exchange, within an integrase binding motif called the extended core binding site. There are four imperfectly repeated copies of this motif in each set of phage attachment sites, but only two, B′ and C, contain major specificity determinants. When these specificity determinants were replaced by the corresponding nucleotides from a site with the alternative specificity, the resulting mutant was recombined by both integrases. Thus, the determinants act by impeding recombination promoted by the non-cognate integrase. We found that identical nucleotide substitutions within different core site copies had different effects on recombination, suggesting that integrase does not recognize each of the extended core binding sites in the same way. Finally, substitution at several positions in λ integrase with the corresponding HK022-specific amino acids prevents recombination of λ attachment sites, and this defect can be suppressed in an allele-specific manner by appropriate substitutions of HK022-specific nucleotides in the extended core binding sites.</description><subject>Amino Acid Sequence</subject><subject>Bacteriophages - enzymology</subject><subject>Binding Sites - genetics</subject><subject>Coliphages - enzymology</subject><subject>DNA-protein interaction</subject><subject>evolution</subject><subject>Integrases - chemistry</subject><subject>Integrases - genetics</subject><subject>lysogeny</subject><subject>Molecular Sequence Data</subject><subject>Mutagenesis - genetics</subject><subject>Plasmids - genetics</subject><subject>Recombination, Genetic - genetics</subject><subject>Sequence Alignment</subject><subject>site-specific recombination</subject><subject>specificity determinants</subject><subject>Viral Proteins - metabolism</subject><issn>0022-2836</issn><issn>1089-8638</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>1998</creationdate><recordtype>article</recordtype><recordid>eNp1kM1LwzAYxoMoc06v3oSevLW-afqRHDyI-AUDQfQckvRNzVibmXTC_ntbN7x5eg7PBzw_Qi4pZBSgull12mVUCJ7RqsiPyJwCFymvGD8mc4A8T3POqlNyFuMKAEpW8BmZibKmozcnt29ofNu7wfk-8TYxPmCiXd-4vk2iGzAmepdoZQYMzm8-VYuJ6wdsg4oYz8mJVeuIFwddkI_Hh_f753T5-vRyf7dMDathSBFsQ5tKFVrkHKgtCyagzimKAlgBioGyurSisVahRg51WbOmVpbnJRuFLcj1fncT_NcW4yA7Fw2u16pHv41yus5Lxsdgtg-a4GMMaOUmuE6FnaQgJ15y4iUnXr-lsXB1WN7qDpu_-AHQ6PO9j-O9b4dBRuOwN9i4gGaQjXf_Tf8AkJ15pg</recordid><startdate>19980417</startdate><enddate>19980417</enddate><creator>Dorgai, László</creator><creator>Sloan, Sieghild</creator><creator>Weisberg, Robert A</creator><general>Elsevier Ltd</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>7U9</scope><scope>H94</scope></search><sort><creationdate>19980417</creationdate><title>Recognition of core binding sites by bacteriophage integrases</title><author>Dorgai, László ; Sloan, Sieghild ; Weisberg, Robert A</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c370t-e0fd1d6a4b92801f54390721e940340a30afb5f9dffaebe807573d7af82537af3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>1998</creationdate><topic>Amino Acid Sequence</topic><topic>Bacteriophages - enzymology</topic><topic>Binding Sites - genetics</topic><topic>Coliphages - enzymology</topic><topic>DNA-protein interaction</topic><topic>evolution</topic><topic>Integrases - chemistry</topic><topic>Integrases - genetics</topic><topic>lysogeny</topic><topic>Molecular Sequence Data</topic><topic>Mutagenesis - genetics</topic><topic>Plasmids - genetics</topic><topic>Recombination, Genetic - genetics</topic><topic>Sequence Alignment</topic><topic>site-specific recombination</topic><topic>specificity determinants</topic><topic>Viral Proteins - metabolism</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Dorgai, László</creatorcontrib><creatorcontrib>Sloan, Sieghild</creatorcontrib><creatorcontrib>Weisberg, Robert A</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>Virology and AIDS Abstracts</collection><collection>AIDS and Cancer Research Abstracts</collection><jtitle>Journal of molecular biology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Dorgai, László</au><au>Sloan, Sieghild</au><au>Weisberg, Robert A</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Recognition of core binding sites by bacteriophage integrases</atitle><jtitle>Journal of molecular biology</jtitle><addtitle>J Mol Biol</addtitle><date>1998-04-17</date><risdate>1998</risdate><volume>277</volume><issue>5</issue><spage>1059</spage><epage>1070</epage><pages>1059-1070</pages><issn>0022-2836</issn><eissn>1089-8638</eissn><abstract>Bacteriophage integrases promote recombination between DNA molecules that carry attachment sites. They are members of a large and widely distributed family of site-specific recombinases with diverse biological roles. The integrases of phages λ and HK022 are closely related members of this family, but neither protein efficiently recombines the attachment sites of the other phage. The nucleotides responsible for this specificity difference are located close to the points of recombinational strand exchange, within an integrase binding motif called the extended core binding site. There are four imperfectly repeated copies of this motif in each set of phage attachment sites, but only two, B′ and C, contain major specificity determinants. When these specificity determinants were replaced by the corresponding nucleotides from a site with the alternative specificity, the resulting mutant was recombined by both integrases. Thus, the determinants act by impeding recombination promoted by the non-cognate integrase. We found that identical nucleotide substitutions within different core site copies had different effects on recombination, suggesting that integrase does not recognize each of the extended core binding sites in the same way. Finally, substitution at several positions in λ integrase with the corresponding HK022-specific amino acids prevents recombination of λ attachment sites, and this defect can be suppressed in an allele-specific manner by appropriate substitutions of HK022-specific nucleotides in the extended core binding sites.</abstract><cop>England</cop><pub>Elsevier Ltd</pub><pmid>9571022</pmid><doi>10.1006/jmbi.1998.1642</doi><tpages>12</tpages></addata></record> |
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subjects | Amino Acid Sequence Bacteriophages - enzymology Binding Sites - genetics Coliphages - enzymology DNA-protein interaction evolution Integrases - chemistry Integrases - genetics lysogeny Molecular Sequence Data Mutagenesis - genetics Plasmids - genetics Recombination, Genetic - genetics Sequence Alignment site-specific recombination specificity determinants Viral Proteins - metabolism |
title | Recognition of core binding sites by bacteriophage integrases |
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