annotated complete DNA sequence of Enterococcus faecalis bacteriophage φEf11 and its comparison with all available phage and predicted prophage genomes
φEf11 is a temperate Siphoviridae bacteriophage isolated by induction from a lysogenic Enterococcus faecalis strain. The φEf11 DNA was completely sequenced and found to be 42 822 bp in length, with a G+C mol% of 34.4%. Genome analysis revealed 65 ORFs, accounting for 92.8% of the DNA content. All ex...
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| creator | Stevens, Roy H Ektefaie, Mahmoud R Fouts, Derrick E |
| description | φEf11 is a temperate Siphoviridae bacteriophage isolated by induction from a lysogenic Enterococcus faecalis strain. The φEf11 DNA was completely sequenced and found to be 42 822 bp in length, with a G+C mol% of 34.4%. Genome analysis revealed 65 ORFs, accounting for 92.8% of the DNA content. All except for seven of the ORFs displayed sequence similarities to previously characterized proteins. The genes were arranged in functional modules, organized similar to that of several other phages of low GC Gram-positive bacteria; however, the number and arrangement of lysis-related genes were atypical of these bacteriophages. A 159 bp noncoding region between predicted cI and cro genes is highly similar to the functionally characterized early promoter region of lactococcal temperate phage TP901-1, and possessed a predicted stem-loop structure in between predicted PL and PR promoters, suggesting a novel mechanism of repression of these two bacteriophages from the λ paradigm. Comparison with all available phage and predicted prophage genomes revealed that the φEf11 genome displays unique features, suggesting that φEf11 may be a novel member of a larger family of temperate prophages that also includes lactococcal phages. Trees based on the blast score ratio grouped this family by tail fiber similarity, suggesting that these trees are useful for identifying phages with similar tail fibers. |
| doi_str_mv | 10.1111/j.1574-6968.2010.02203.x |
| format | Article |
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The φEf11 DNA was completely sequenced and found to be 42 822 bp in length, with a G+C mol% of 34.4%. Genome analysis revealed 65 ORFs, accounting for 92.8% of the DNA content. All except for seven of the ORFs displayed sequence similarities to previously characterized proteins. The genes were arranged in functional modules, organized similar to that of several other phages of low GC Gram-positive bacteria; however, the number and arrangement of lysis-related genes were atypical of these bacteriophages. A 159 bp noncoding region between predicted cI and cro genes is highly similar to the functionally characterized early promoter region of lactococcal temperate phage TP901-1, and possessed a predicted stem-loop structure in between predicted PL and PR promoters, suggesting a novel mechanism of repression of these two bacteriophages from the λ paradigm. Comparison with all available phage and predicted prophage genomes revealed that the φEf11 genome displays unique features, suggesting that φEf11 may be a novel member of a larger family of temperate prophages that also includes lactococcal phages. Trees based on the blast score ratio grouped this family by tail fiber similarity, suggesting that these trees are useful for identifying phages with similar tail fibers.</description><identifier>ISSN: 0378-1097</identifier><identifier>EISSN: 1574-6968</identifier><identifier>DOI: 10.1111/j.1574-6968.2010.02203.x</identifier><identifier>PMID: 21204936</identifier><identifier>CODEN: FMLED7</identifier><language>eng</language><publisher>Oxford, UK: Blackwell Publishing Ltd</publisher><subject>Bacteria ; Bacteriology ; bacteriophage φEf11 ; Base Composition ; Biological and medical sciences ; Cluster Analysis ; Deoxyribonucleic acid ; DNA ; DNA, Viral - chemistry ; DNA, Viral - genetics ; Enterococcus faecalis ; Enterococcus faecalis - virology ; Fundamental and applied biological sciences. Psychology ; Gene Order ; Genes ; Genome, Viral ; Genomes ; Gram-positive bacteria ; Lysis ; Microbiology ; Miscellaneous ; Molecular Sequence Data ; Nucleotide sequence ; Open Reading Frames - genetics ; phage genome sequence and analysis ; Phages ; Phylogeny ; Promoter Regions, Genetic ; Prophages ; Prophages - genetics ; Prophages - isolation & purification ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Siphoviridae ; Synteny ; Tail fiber protein ; Trees ; Virology</subject><ispartof>FEMS microbiology letters, 2011-04, Vol.317 (1), p.9-26</ispartof><rights>2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved 2011</rights><rights>2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved</rights><rights>2015 INIST-CNRS</rights><rights>2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c3923-41eef92db4b13be2e5b7a220b199fb4902243f8491ea90e963de5235a06a6eab3</citedby></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.1574-6968.2010.02203.x$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1111%2Fj.1574-6968.2010.02203.x$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>314,776,780,1411,27901,27902,45550,45551</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=23912650$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/21204936$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Stevens, Roy H</creatorcontrib><creatorcontrib>Ektefaie, Mahmoud R</creatorcontrib><creatorcontrib>Fouts, Derrick E</creatorcontrib><title>annotated complete DNA sequence of Enterococcus faecalis bacteriophage φEf11 and its comparison with all available phage and predicted prophage genomes</title><title>FEMS microbiology letters</title><addtitle>FEMS Microbiol Lett</addtitle><description>φEf11 is a temperate Siphoviridae bacteriophage isolated by induction from a lysogenic Enterococcus faecalis strain. The φEf11 DNA was completely sequenced and found to be 42 822 bp in length, with a G+C mol% of 34.4%. Genome analysis revealed 65 ORFs, accounting for 92.8% of the DNA content. All except for seven of the ORFs displayed sequence similarities to previously characterized proteins. The genes were arranged in functional modules, organized similar to that of several other phages of low GC Gram-positive bacteria; however, the number and arrangement of lysis-related genes were atypical of these bacteriophages. A 159 bp noncoding region between predicted cI and cro genes is highly similar to the functionally characterized early promoter region of lactococcal temperate phage TP901-1, and possessed a predicted stem-loop structure in between predicted PL and PR promoters, suggesting a novel mechanism of repression of these two bacteriophages from the λ paradigm. Comparison with all available phage and predicted prophage genomes revealed that the φEf11 genome displays unique features, suggesting that φEf11 may be a novel member of a larger family of temperate prophages that also includes lactococcal phages. Trees based on the blast score ratio grouped this family by tail fiber similarity, suggesting that these trees are useful for identifying phages with similar tail fibers.</description><subject>Bacteria</subject><subject>Bacteriology</subject><subject>bacteriophage φEf11</subject><subject>Base Composition</subject><subject>Biological and medical sciences</subject><subject>Cluster Analysis</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA, Viral - chemistry</subject><subject>DNA, Viral - genetics</subject><subject>Enterococcus faecalis</subject><subject>Enterococcus faecalis - virology</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Gene Order</subject><subject>Genes</subject><subject>Genome, Viral</subject><subject>Genomes</subject><subject>Gram-positive bacteria</subject><subject>Lysis</subject><subject>Microbiology</subject><subject>Miscellaneous</subject><subject>Molecular Sequence Data</subject><subject>Nucleotide sequence</subject><subject>Open Reading Frames - genetics</subject><subject>phage genome sequence and analysis</subject><subject>Phages</subject><subject>Phylogeny</subject><subject>Promoter Regions, Genetic</subject><subject>Prophages</subject><subject>Prophages - genetics</subject><subject>Prophages - isolation & purification</subject><subject>Sequence Analysis, DNA</subject><subject>Sequence Homology, Amino Acid</subject><subject>Siphoviridae</subject><subject>Synteny</subject><subject>Tail fiber protein</subject><subject>Trees</subject><subject>Virology</subject><issn>0378-1097</issn><issn>1574-6968</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2011</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><recordid>eNqFks1u1DAQxy0EokvhFcASqjhl8Ue-fOBQlS0gLXCAnq2xM9l6lcQhTmj7AjwDb8Ur4TRLkUAIX2x5fv-xZ-ZPCOVszeN6uV_zrEiTXOXlWrB4y4Rgcn19j6zuAvfJismiTDhTxRF5FMKeMZYKlj8kR4ILliqZr8h36Do_wogVtb7tGxyRvv5wSgN-mbCzSH1NN92Ig7fe2inQGtBC4wI1YOO18_0l7JD--LapOafQVdSN4TYXDC74jl658ZJC01D4Cq4B0yBdJDPbD1g5O7_eD4dMO-x8i-ExeVBDE_DJYT8mF-ebz2dvk-3HN-_OTreJlUrIJOWItRKVSQ2XBgVmpoDYDMOVqk2qYmNSWZep4giKocplhZmQGbAccgQjj8mLJW_8QCw5jLp1wWLTQId-CjpmkHnBCvFfssyy-CjPs0g-_4Pc-2noYhlaSJaVZRkHE6mnB2oyLVa6H1wLw43-NZwInBwACLHn9QCddeE3JxUXecYi92rhrlyDN3dxzvRsFr3Xsyf07Ak9m0XfmkVf6_P32_kU9XLR-6n_hzr5Sx1VzxZVDV7DLg5bX3yKhGRcpUpkqfwJYt3LXw</recordid><startdate>201104</startdate><enddate>201104</enddate><creator>Stevens, Roy H</creator><creator>Ektefaie, Mahmoud R</creator><creator>Fouts, Derrick E</creator><general>Blackwell Publishing Ltd</general><general>Wiley-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>PHGZM</scope><scope>PHGZT</scope><scope>PJZUB</scope><scope>PKEHL</scope><scope>PPXIY</scope><scope>PQEST</scope><scope>PQGLB</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>RC3</scope><scope>7X8</scope></search><sort><creationdate>201104</creationdate><title>annotated complete DNA sequence of Enterococcus faecalis bacteriophage φEf11 and its comparison with all available phage and predicted prophage genomes</title><author>Stevens, Roy H ; Ektefaie, Mahmoud R ; Fouts, Derrick E</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c3923-41eef92db4b13be2e5b7a220b199fb4902243f8491ea90e963de5235a06a6eab3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2011</creationdate><topic>Bacteria</topic><topic>Bacteriology</topic><topic>bacteriophage φEf11</topic><topic>Base Composition</topic><topic>Biological and medical sciences</topic><topic>Cluster Analysis</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>DNA, Viral - chemistry</topic><topic>DNA, Viral - genetics</topic><topic>Enterococcus faecalis</topic><topic>Enterococcus faecalis - virology</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>Gene Order</topic><topic>Genes</topic><topic>Genome, Viral</topic><topic>Genomes</topic><topic>Gram-positive bacteria</topic><topic>Lysis</topic><topic>Microbiology</topic><topic>Miscellaneous</topic><topic>Molecular Sequence Data</topic><topic>Nucleotide sequence</topic><topic>Open Reading Frames - genetics</topic><topic>phage genome sequence and analysis</topic><topic>Phages</topic><topic>Phylogeny</topic><topic>Promoter Regions, Genetic</topic><topic>Prophages</topic><topic>Prophages - genetics</topic><topic>Prophages - isolation & purification</topic><topic>Sequence Analysis, DNA</topic><topic>Sequence Homology, Amino Acid</topic><topic>Siphoviridae</topic><topic>Synteny</topic><topic>Tail fiber protein</topic><topic>Trees</topic><topic>Virology</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Stevens, Roy H</creatorcontrib><creatorcontrib>Ektefaie, Mahmoud R</creatorcontrib><creatorcontrib>Fouts, Derrick E</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 Central (New)</collection><collection>ProQuest One Academic (New)</collection><collection>ProQuest Health & Medical Research Collection</collection><collection>ProQuest One Academic Middle East (New)</collection><collection>ProQuest One Health & Nursing</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Applied & Life Sciences</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>FEMS microbiology letters</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Stevens, Roy H</au><au>Ektefaie, Mahmoud R</au><au>Fouts, Derrick E</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>annotated complete DNA sequence of Enterococcus faecalis bacteriophage φEf11 and its comparison with all available phage and predicted prophage genomes</atitle><jtitle>FEMS microbiology letters</jtitle><addtitle>FEMS Microbiol Lett</addtitle><date>2011-04</date><risdate>2011</risdate><volume>317</volume><issue>1</issue><spage>9</spage><epage>26</epage><pages>9-26</pages><issn>0378-1097</issn><eissn>1574-6968</eissn><coden>FMLED7</coden><abstract>φEf11 is a temperate Siphoviridae bacteriophage isolated by induction from a lysogenic Enterococcus faecalis strain. The φEf11 DNA was completely sequenced and found to be 42 822 bp in length, with a G+C mol% of 34.4%. Genome analysis revealed 65 ORFs, accounting for 92.8% of the DNA content. All except for seven of the ORFs displayed sequence similarities to previously characterized proteins. The genes were arranged in functional modules, organized similar to that of several other phages of low GC Gram-positive bacteria; however, the number and arrangement of lysis-related genes were atypical of these bacteriophages. A 159 bp noncoding region between predicted cI and cro genes is highly similar to the functionally characterized early promoter region of lactococcal temperate phage TP901-1, and possessed a predicted stem-loop structure in between predicted PL and PR promoters, suggesting a novel mechanism of repression of these two bacteriophages from the λ paradigm. Comparison with all available phage and predicted prophage genomes revealed that the φEf11 genome displays unique features, suggesting that φEf11 may be a novel member of a larger family of temperate prophages that also includes lactococcal phages. Trees based on the blast score ratio grouped this family by tail fiber similarity, suggesting that these trees are useful for identifying phages with similar tail fibers.</abstract><cop>Oxford, UK</cop><pub>Blackwell Publishing Ltd</pub><pmid>21204936</pmid><doi>10.1111/j.1574-6968.2010.02203.x</doi><tpages>18</tpages></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 0378-1097 |
| ispartof | FEMS microbiology letters, 2011-04, Vol.317 (1), p.9-26 |
| issn | 0378-1097 1574-6968 |
| language | eng |
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| source | Oxford University Press Journals All Titles (1996-Current); MEDLINE; Wiley Online Library Journals Frontfile Complete |
| subjects | Bacteria Bacteriology bacteriophage φEf11 Base Composition Biological and medical sciences Cluster Analysis Deoxyribonucleic acid DNA DNA, Viral - chemistry DNA, Viral - genetics Enterococcus faecalis Enterococcus faecalis - virology Fundamental and applied biological sciences. Psychology Gene Order Genes Genome, Viral Genomes Gram-positive bacteria Lysis Microbiology Miscellaneous Molecular Sequence Data Nucleotide sequence Open Reading Frames - genetics phage genome sequence and analysis Phages Phylogeny Promoter Regions, Genetic Prophages Prophages - genetics Prophages - isolation & purification Sequence Analysis, DNA Sequence Homology, Amino Acid Siphoviridae Synteny Tail fiber protein Trees Virology |
| title | annotated complete DNA sequence of Enterococcus faecalis bacteriophage φEf11 and its comparison with all available phage and predicted prophage genomes |
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