orf4 gene of the enterobacterial ICE, R391, encodes a novel UV-inducible recombination directionality factor, Jef, involved in excision and transfer of the ICE
The enterobacterial mobile genetic element R391, the prototype ICE (integrating-conjugative element) of the SXT/R391 family, shows increased conjugative transfer following UV irradiation. This is dependent on a functioning R391 orf4 gene, which is adjacent to the element encoded integrase gene, int....
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description | The enterobacterial mobile genetic element R391, the prototype ICE (integrating-conjugative element) of the SXT/R391 family, shows increased conjugative transfer following UV irradiation. This is dependent on a functioning R391 orf4 gene, which is adjacent to the element encoded integrase gene, int. orf4 mutants fail to form a detectable circular transfer intermediate, do not show UV induced transfer and show a much reduced general transfer ability. The orf4 gene product, termed Jef (IncJ excision factor), shows little homology to anything currently in the nucleotide or protein databases. It is predicted to encode a 66 amino acid, 8.03 kDa, basic, DNA-binding protein with an iso-electric point of pH 8.1: these characteristics being similar to those of recombinational directionality factors involved in excision. Jef expression is up-regulated upon UV irradiation as demonstrated by real-time reverse transcriptase PCR and is controlled by two element encoded genes orf90 and orf91, which show similarity to the transcriptional activator complex FlhC and FlhD. orf4, orf90 and orf91 are conserved in all the SXT/R391-like elements sequenced to date including SXT, ICESpuPO1 and ICEVchMex1. orf4 is also conserved in other SXT/R391 family members such as R997, R392, R705 and pMERPH as shown by sequencing amplicons from these ICEs generated using orf4 specific primers. |
doi_str_mv | 10.1111/j.1574-6968.2007.00747.x |
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Tony</creator><creatorcontrib>O'Halloran, John A ; McGrath, Barry M ; Pembroke, J. Tony</creatorcontrib><description>The enterobacterial mobile genetic element R391, the prototype ICE (integrating-conjugative element) of the SXT/R391 family, shows increased conjugative transfer following UV irradiation. This is dependent on a functioning R391 orf4 gene, which is adjacent to the element encoded integrase gene, int. orf4 mutants fail to form a detectable circular transfer intermediate, do not show UV induced transfer and show a much reduced general transfer ability. The orf4 gene product, termed Jef (IncJ excision factor), shows little homology to anything currently in the nucleotide or protein databases. It is predicted to encode a 66 amino acid, 8.03 kDa, basic, DNA-binding protein with an iso-electric point of pH 8.1: these characteristics being similar to those of recombinational directionality factors involved in excision. Jef expression is up-regulated upon UV irradiation as demonstrated by real-time reverse transcriptase PCR and is controlled by two element encoded genes orf90 and orf91, which show similarity to the transcriptional activator complex FlhC and FlhD. orf4, orf90 and orf91 are conserved in all the SXT/R391-like elements sequenced to date including SXT, ICESpuPO1 and ICEVchMex1. orf4 is also conserved in other SXT/R391 family members such as R997, R392, R705 and pMERPH as shown by sequencing amplicons from these ICEs generated using orf4 specific primers.</description><identifier>ISSN: 0378-1097</identifier><identifier>EISSN: 1574-6968</identifier><identifier>DOI: 10.1111/j.1574-6968.2007.00747.x</identifier><identifier>PMID: 17504243</identifier><identifier>CODEN: FMLED7</identifier><language>eng</language><publisher>Oxford, UK: Oxford, UK : Blackwell Publishing Ltd</publisher><subject>Amino Acid Sequence ; Amino acids ; Bacterial Proteins - biosynthesis ; Bacterial Proteins - genetics ; Bacterial Proteins - physiology ; Bacteriology ; Biological and medical sciences ; Conjugation, Genetic - genetics ; Conserved Sequence - genetics ; Deoxyribonucleic acid ; DNA ; DNA, Bacterial - chemistry ; DNA, Bacterial - genetics ; DNA-binding protein ; Enterobacteriaceae - genetics ; Enterobacteriaceae - physiology ; Enterobacteriaceae - radiation effects ; Fundamental and applied biological sciences. Psychology ; Gene Deletion ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal - genetics ; Genetics ; Homology ; Integrase ; Interspersed Repetitive Sequences ; Irradiation ; Isoelectric Point ; Microbiology ; Molecular Sequence Data ; Molecular Weight ; Mutagenesis, Insertional ; Nucleotides ; Orf4 gene ; Proteins ; Recombination ; recombination directionality factor Jef ; Recombination, Genetic ; Reverse Transcriptase Polymerase Chain Reaction ; RNA, Bacterial - biosynthesis ; RNA, Bacterial - genetics ; RNA, Messenger - biosynthesis ; RNA, Messenger - genetics ; RNA-directed DNA polymerase ; Sequence Analysis, DNA ; Sequence Homology ; SXT/R391 ICE elements ; Transcription ; Ultraviolet radiation ; Ultraviolet Rays ; UV-induced conjugative transfer</subject><ispartof>FEMS microbiology letters, 2007-07, Vol.272 (1), p.99-105</ispartof><rights>2007 Federation of European Microbiological Societies Published by Blackwell Publishing Ltd. All rights reserved 2007</rights><rights>2007 INIST-CNRS</rights><rights>2007 Federation of European Microbiological Societies Published by Blackwell Publishing Ltd. All rights reserved</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1111%2Fj.1574-6968.2007.00747.x$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1111%2Fj.1574-6968.2007.00747.x$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>314,780,784,1416,27923,27924,45573,45574</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=18799843$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/17504243$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>O'Halloran, John A</creatorcontrib><creatorcontrib>McGrath, Barry M</creatorcontrib><creatorcontrib>Pembroke, J. Tony</creatorcontrib><title>orf4 gene of the enterobacterial ICE, R391, encodes a novel UV-inducible recombination directionality factor, Jef, involved in excision and transfer of the ICE</title><title>FEMS microbiology letters</title><addtitle>FEMS Microbiol Lett</addtitle><description>The enterobacterial mobile genetic element R391, the prototype ICE (integrating-conjugative element) of the SXT/R391 family, shows increased conjugative transfer following UV irradiation. This is dependent on a functioning R391 orf4 gene, which is adjacent to the element encoded integrase gene, int. orf4 mutants fail to form a detectable circular transfer intermediate, do not show UV induced transfer and show a much reduced general transfer ability. The orf4 gene product, termed Jef (IncJ excision factor), shows little homology to anything currently in the nucleotide or protein databases. It is predicted to encode a 66 amino acid, 8.03 kDa, basic, DNA-binding protein with an iso-electric point of pH 8.1: these characteristics being similar to those of recombinational directionality factors involved in excision. Jef expression is up-regulated upon UV irradiation as demonstrated by real-time reverse transcriptase PCR and is controlled by two element encoded genes orf90 and orf91, which show similarity to the transcriptional activator complex FlhC and FlhD. orf4, orf90 and orf91 are conserved in all the SXT/R391-like elements sequenced to date including SXT, ICESpuPO1 and ICEVchMex1. orf4 is also conserved in other SXT/R391 family members such as R997, R392, R705 and pMERPH as shown by sequencing amplicons from these ICEs generated using orf4 specific primers.</description><subject>Amino Acid Sequence</subject><subject>Amino acids</subject><subject>Bacterial Proteins - biosynthesis</subject><subject>Bacterial Proteins - genetics</subject><subject>Bacterial Proteins - physiology</subject><subject>Bacteriology</subject><subject>Biological and medical sciences</subject><subject>Conjugation, Genetic - genetics</subject><subject>Conserved Sequence - genetics</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA, Bacterial - chemistry</subject><subject>DNA, Bacterial - genetics</subject><subject>DNA-binding protein</subject><subject>Enterobacteriaceae - genetics</subject><subject>Enterobacteriaceae - physiology</subject><subject>Enterobacteriaceae - radiation effects</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Gene Deletion</subject><subject>Gene Expression Regulation, Bacterial</subject><subject>Gene Transfer, Horizontal - genetics</subject><subject>Genetics</subject><subject>Homology</subject><subject>Integrase</subject><subject>Interspersed Repetitive Sequences</subject><subject>Irradiation</subject><subject>Isoelectric Point</subject><subject>Microbiology</subject><subject>Molecular Sequence Data</subject><subject>Molecular Weight</subject><subject>Mutagenesis, Insertional</subject><subject>Nucleotides</subject><subject>Orf4 gene</subject><subject>Proteins</subject><subject>Recombination</subject><subject>recombination directionality factor Jef</subject><subject>Recombination, Genetic</subject><subject>Reverse Transcriptase Polymerase Chain Reaction</subject><subject>RNA, Bacterial - biosynthesis</subject><subject>RNA, Bacterial - genetics</subject><subject>RNA, Messenger - biosynthesis</subject><subject>RNA, Messenger - genetics</subject><subject>RNA-directed DNA polymerase</subject><subject>Sequence Analysis, DNA</subject><subject>Sequence Homology</subject><subject>SXT/R391 ICE elements</subject><subject>Transcription</subject><subject>Ultraviolet radiation</subject><subject>Ultraviolet Rays</subject><subject>UV-induced conjugative transfer</subject><issn>0378-1097</issn><issn>1574-6968</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2007</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNp1km1v0zAQxyMEYmXwFcASgldN8EMSOxJvULXBUBESUN5ajnMertK4c5LSfhq-Kpe1YxIIS5bPut__fHe-JCGMZgzXm3XGCpmnZVWqjFMqM9y5zPYPktkfx8NkRoVUKaOVPEue9P2aUppzWj5Ozpgs0MzFLPkVosvJNXRAgiPDDyDQDRBDbSwe3rTkanExJ19ExebosqGBnhjShR20ZPU99V0zWl-3QCLYsKl9ZwYfOtJ4vE-Waf1wIA7DhTgnH8HNie92od1BgwaBvfX9JDBdQ4Zout5BvEsFn36aPHKm7eHZ6TxPVpcX3xYf0uXn91eLd8vU5aySKSssmIorlnOljLWK1UJIaTkvQVEjXQGsdopT6_IcTAm8sKV0JqdlUZRGiPPk9THuNoabEfpBb3xvoW1NB2HsNaeKllIoBF_-Ba7DGLFMZARGE9juKdzzEzXWG2j0NvqNiQd913gEXp0A01vTOqwcG3HPKVlV6pZ7e-R--hYO936qp0HQaz39t57-W0-DoG8HQe_15aclGigXR3kYt_8Rp_-IUfXiqHImaHMdMbHVV06ZQEDlJZfiN6gGvRc</recordid><startdate>200707</startdate><enddate>200707</enddate><creator>O'Halloran, John A</creator><creator>McGrath, Barry M</creator><creator>Pembroke, J. Tony</creator><general>Oxford, UK : Blackwell Publishing Ltd</general><general>Blackwell Publishing Ltd</general><general>Blackwell</general><general>Oxford University Press</general><scope>FBQ</scope><scope>IQODW</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>3V.</scope><scope>7QL</scope><scope>7T7</scope><scope>7TK</scope><scope>7TM</scope><scope>7U9</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>P64</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>RC3</scope></search><sort><creationdate>200707</creationdate><title>orf4 gene of the enterobacterial ICE, R391, encodes a novel UV-inducible recombination directionality factor, Jef, involved in excision and transfer of the ICE</title><author>O'Halloran, John A ; McGrath, Barry M ; Pembroke, J. Tony</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-f4197-15cea92814288acc81b3377c226e80a7f5e1bf820cf44ea6e25c67fa406556a33</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2007</creationdate><topic>Amino Acid Sequence</topic><topic>Amino acids</topic><topic>Bacterial Proteins - biosynthesis</topic><topic>Bacterial Proteins - genetics</topic><topic>Bacterial Proteins - physiology</topic><topic>Bacteriology</topic><topic>Biological and medical sciences</topic><topic>Conjugation, Genetic - genetics</topic><topic>Conserved Sequence - genetics</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>DNA, Bacterial - chemistry</topic><topic>DNA, Bacterial - genetics</topic><topic>DNA-binding protein</topic><topic>Enterobacteriaceae - genetics</topic><topic>Enterobacteriaceae - physiology</topic><topic>Enterobacteriaceae - radiation effects</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>Gene Deletion</topic><topic>Gene Expression Regulation, Bacterial</topic><topic>Gene Transfer, Horizontal - genetics</topic><topic>Genetics</topic><topic>Homology</topic><topic>Integrase</topic><topic>Interspersed Repetitive Sequences</topic><topic>Irradiation</topic><topic>Isoelectric Point</topic><topic>Microbiology</topic><topic>Molecular Sequence Data</topic><topic>Molecular Weight</topic><topic>Mutagenesis, Insertional</topic><topic>Nucleotides</topic><topic>Orf4 gene</topic><topic>Proteins</topic><topic>Recombination</topic><topic>recombination directionality factor Jef</topic><topic>Recombination, Genetic</topic><topic>Reverse Transcriptase Polymerase Chain Reaction</topic><topic>RNA, Bacterial - biosynthesis</topic><topic>RNA, Bacterial - genetics</topic><topic>RNA, Messenger - biosynthesis</topic><topic>RNA, Messenger - genetics</topic><topic>RNA-directed DNA polymerase</topic><topic>Sequence Analysis, DNA</topic><topic>Sequence Homology</topic><topic>SXT/R391 ICE elements</topic><topic>Transcription</topic><topic>Ultraviolet radiation</topic><topic>Ultraviolet Rays</topic><topic>UV-induced conjugative transfer</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>O'Halloran, John A</creatorcontrib><creatorcontrib>McGrath, Barry M</creatorcontrib><creatorcontrib>Pembroke, J. Tony</creatorcontrib><collection>AGRIS</collection><collection>Pascal-Francis</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>ProQuest Central (Corporate)</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Neurosciences Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Public Health Database</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest One Sustainability</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biological Science Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>Genetics Abstracts</collection><jtitle>FEMS microbiology letters</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>O'Halloran, John A</au><au>McGrath, Barry M</au><au>Pembroke, J. Tony</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>orf4 gene of the enterobacterial ICE, R391, encodes a novel UV-inducible recombination directionality factor, Jef, involved in excision and transfer of the ICE</atitle><jtitle>FEMS microbiology letters</jtitle><addtitle>FEMS Microbiol Lett</addtitle><date>2007-07</date><risdate>2007</risdate><volume>272</volume><issue>1</issue><spage>99</spage><epage>105</epage><pages>99-105</pages><issn>0378-1097</issn><eissn>1574-6968</eissn><coden>FMLED7</coden><abstract>The enterobacterial mobile genetic element R391, the prototype ICE (integrating-conjugative element) of the SXT/R391 family, shows increased conjugative transfer following UV irradiation. This is dependent on a functioning R391 orf4 gene, which is adjacent to the element encoded integrase gene, int. orf4 mutants fail to form a detectable circular transfer intermediate, do not show UV induced transfer and show a much reduced general transfer ability. The orf4 gene product, termed Jef (IncJ excision factor), shows little homology to anything currently in the nucleotide or protein databases. It is predicted to encode a 66 amino acid, 8.03 kDa, basic, DNA-binding protein with an iso-electric point of pH 8.1: these characteristics being similar to those of recombinational directionality factors involved in excision. Jef expression is up-regulated upon UV irradiation as demonstrated by real-time reverse transcriptase PCR and is controlled by two element encoded genes orf90 and orf91, which show similarity to the transcriptional activator complex FlhC and FlhD. orf4, orf90 and orf91 are conserved in all the SXT/R391-like elements sequenced to date including SXT, ICESpuPO1 and ICEVchMex1. orf4 is also conserved in other SXT/R391 family members such as R997, R392, R705 and pMERPH as shown by sequencing amplicons from these ICEs generated using orf4 specific primers.</abstract><cop>Oxford, UK</cop><pub>Oxford, UK : Blackwell Publishing Ltd</pub><pmid>17504243</pmid><doi>10.1111/j.1574-6968.2007.00747.x</doi><tpages>7</tpages></addata></record> |
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source | MEDLINE; Oxford University Press Journals All Titles (1996-Current); Wiley Online Library All Journals |
subjects | Amino Acid Sequence Amino acids Bacterial Proteins - biosynthesis Bacterial Proteins - genetics Bacterial Proteins - physiology Bacteriology Biological and medical sciences Conjugation, Genetic - genetics Conserved Sequence - genetics Deoxyribonucleic acid DNA DNA, Bacterial - chemistry DNA, Bacterial - genetics DNA-binding protein Enterobacteriaceae - genetics Enterobacteriaceae - physiology Enterobacteriaceae - radiation effects Fundamental and applied biological sciences. Psychology Gene Deletion Gene Expression Regulation, Bacterial Gene Transfer, Horizontal - genetics Genetics Homology Integrase Interspersed Repetitive Sequences Irradiation Isoelectric Point Microbiology Molecular Sequence Data Molecular Weight Mutagenesis, Insertional Nucleotides Orf4 gene Proteins Recombination recombination directionality factor Jef Recombination, Genetic Reverse Transcriptase Polymerase Chain Reaction RNA, Bacterial - biosynthesis RNA, Bacterial - genetics RNA, Messenger - biosynthesis RNA, Messenger - genetics RNA-directed DNA polymerase Sequence Analysis, DNA Sequence Homology SXT/R391 ICE elements Transcription Ultraviolet radiation Ultraviolet Rays UV-induced conjugative transfer |
title | orf4 gene of the enterobacterial ICE, R391, encodes a novel UV-inducible recombination directionality factor, Jef, involved in excision and transfer of the ICE |
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