Genome Comparison of Pseudomonas aeruginosa Large Phages
Pseudomonas aeruginosa phage EL is a dsDNA phage related to the giant ϕKZ-like Myoviridae. The EL genome sequence comprises 211,215 bp and has 201 predicted open reading frames (ORFs). The EL genome does not share DNA sequence homology with other viruses and micro-organisms sequenced to date. Howeve...
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| Veröffentlicht in: | Journal of molecular biology 2005-12, Vol.354 (3), p.536-545 |
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| creator | Hertveldt, Kirsten Lavigne, Rob Pleteneva, Elena Sernova, Natalia Kurochkina, Lidia Korchevskii, Roman Robben, Johan Mesyanzhinov, Vadim Krylov, Victor N. Volckaert, Guido |
| description | Pseudomonas aeruginosa phage EL is a dsDNA phage related to the giant ϕKZ-like Myoviridae. The EL genome sequence comprises 211,215
bp and has 201 predicted open reading frames (ORFs). The EL genome does not share DNA sequence homology with other viruses and micro-organisms sequenced to date. However, one-third of the predicted EL gene products (gps) shares similarity (Blast alignments of 17–55% amino acid identity) with ϕKZ proteins. Comparative EL and ϕKZ genomics reveals that these giant phages are an example of substantially diverged genetic mosaics. Based on the position of similar EL and ϕKZ predicted gene products, five genome regions can be delineated in EL, four of which are relatively conserved between EL and ϕKZ. Region IV, a 17.7
kb genome region with 28 predicted ORFs, is unique to EL. Fourteen EL ORFs have been assigned a putative function based on protein similarity. Assigned proteins are involved in DNA replication and nucleotide metabolism (NAD
+-dependent DNA ligase, ribonuclease HI, helicase, thymidylate kinase), host lysis and particle structure. EL-gp146 is the first chaperonin GroEL sequence identified in a viral genome. Besides a putative transposase, EL harbours predicted mobile endonucleases related to H–N–H and LAGLIDADG homing endonucleases associated with group I intron and intein intervening sequences. |
| doi_str_mv | 10.1016/j.jmb.2005.08.075 |
| format | Article |
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bp and has 201 predicted open reading frames (ORFs). The EL genome does not share DNA sequence homology with other viruses and micro-organisms sequenced to date. However, one-third of the predicted EL gene products (gps) shares similarity (Blast alignments of 17–55% amino acid identity) with ϕKZ proteins. Comparative EL and ϕKZ genomics reveals that these giant phages are an example of substantially diverged genetic mosaics. Based on the position of similar EL and ϕKZ predicted gene products, five genome regions can be delineated in EL, four of which are relatively conserved between EL and ϕKZ. Region IV, a 17.7
kb genome region with 28 predicted ORFs, is unique to EL. Fourteen EL ORFs have been assigned a putative function based on protein similarity. Assigned proteins are involved in DNA replication and nucleotide metabolism (NAD
+-dependent DNA ligase, ribonuclease HI, helicase, thymidylate kinase), host lysis and particle structure. EL-gp146 is the first chaperonin GroEL sequence identified in a viral genome. Besides a putative transposase, EL harbours predicted mobile endonucleases related to H–N–H and LAGLIDADG homing endonucleases associated with group I intron and intein intervening sequences.</description><identifier>ISSN: 0022-2836</identifier><identifier>EISSN: 1089-8638</identifier><identifier>DOI: 10.1016/j.jmb.2005.08.075</identifier><identifier>PMID: 16256135</identifier><language>eng</language><publisher>England: Elsevier Ltd</publisher><subject>Amino Acid Sequence ; bacteriophage genomics ; DNA Replication - genetics ; Endonucleases - metabolism ; Genes, Viral - genetics ; Genome, Viral - genetics ; homing endonuclease ; Inteins ; Microscopy, Electron ; Molecular Sequence Data ; Myoviridae ; Myovirus ; Open Reading Frames - genetics ; phage EL ; phage evolution ; phage ϕKZ ; Pseudomonas aeruginosa ; Pseudomonas aeruginosa - ultrastructure ; Pseudomonas aeruginosa - virology ; Pseudomonas Phages - genetics ; Pseudomonas Phages - ultrastructure ; Sequence Alignment ; Sequence Homology, Amino Acid ; Transcription, Genetic - genetics ; Viral Proteins - genetics ; Virus Activation</subject><ispartof>Journal of molecular biology, 2005-12, Vol.354 (3), p.536-545</ispartof><rights>2005 Elsevier Ltd</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c448t-cbe00ad70d46974a274615ffad8a513c45ffb3d6da4dece90266ddf39e1f45723</citedby><cites>FETCH-LOGICAL-c448t-cbe00ad70d46974a274615ffad8a513c45ffb3d6da4dece90266ddf39e1f45723</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://dx.doi.org/10.1016/j.jmb.2005.08.075$$EHTML$$P50$$Gelsevier$$H</linktohtml><link.rule.ids>314,780,784,3549,27923,27924,45994</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/16256135$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Hertveldt, Kirsten</creatorcontrib><creatorcontrib>Lavigne, Rob</creatorcontrib><creatorcontrib>Pleteneva, Elena</creatorcontrib><creatorcontrib>Sernova, Natalia</creatorcontrib><creatorcontrib>Kurochkina, Lidia</creatorcontrib><creatorcontrib>Korchevskii, Roman</creatorcontrib><creatorcontrib>Robben, Johan</creatorcontrib><creatorcontrib>Mesyanzhinov, Vadim</creatorcontrib><creatorcontrib>Krylov, Victor N.</creatorcontrib><creatorcontrib>Volckaert, Guido</creatorcontrib><title>Genome Comparison of Pseudomonas aeruginosa Large Phages</title><title>Journal of molecular biology</title><addtitle>J Mol Biol</addtitle><description>Pseudomonas aeruginosa phage EL is a dsDNA phage related to the giant ϕKZ-like Myoviridae. The EL genome sequence comprises 211,215
bp and has 201 predicted open reading frames (ORFs). The EL genome does not share DNA sequence homology with other viruses and micro-organisms sequenced to date. However, one-third of the predicted EL gene products (gps) shares similarity (Blast alignments of 17–55% amino acid identity) with ϕKZ proteins. Comparative EL and ϕKZ genomics reveals that these giant phages are an example of substantially diverged genetic mosaics. Based on the position of similar EL and ϕKZ predicted gene products, five genome regions can be delineated in EL, four of which are relatively conserved between EL and ϕKZ. Region IV, a 17.7
kb genome region with 28 predicted ORFs, is unique to EL. Fourteen EL ORFs have been assigned a putative function based on protein similarity. Assigned proteins are involved in DNA replication and nucleotide metabolism (NAD
+-dependent DNA ligase, ribonuclease HI, helicase, thymidylate kinase), host lysis and particle structure. EL-gp146 is the first chaperonin GroEL sequence identified in a viral genome. Besides a putative transposase, EL harbours predicted mobile endonucleases related to H–N–H and LAGLIDADG homing endonucleases associated with group I intron and intein intervening sequences.</description><subject>Amino Acid Sequence</subject><subject>bacteriophage genomics</subject><subject>DNA Replication - genetics</subject><subject>Endonucleases - metabolism</subject><subject>Genes, Viral - genetics</subject><subject>Genome, Viral - genetics</subject><subject>homing endonuclease</subject><subject>Inteins</subject><subject>Microscopy, Electron</subject><subject>Molecular Sequence Data</subject><subject>Myoviridae</subject><subject>Myovirus</subject><subject>Open Reading Frames - genetics</subject><subject>phage EL</subject><subject>phage evolution</subject><subject>phage ϕKZ</subject><subject>Pseudomonas aeruginosa</subject><subject>Pseudomonas aeruginosa - ultrastructure</subject><subject>Pseudomonas aeruginosa - virology</subject><subject>Pseudomonas Phages - genetics</subject><subject>Pseudomonas Phages - ultrastructure</subject><subject>Sequence Alignment</subject><subject>Sequence Homology, Amino Acid</subject><subject>Transcription, Genetic - genetics</subject><subject>Viral Proteins - genetics</subject><subject>Virus Activation</subject><issn>0022-2836</issn><issn>1089-8638</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2005</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqNkLFOwzAURS0EoqXwASwoE1uC7diOIyZUQUGqRAeYLcd-KY6auNgNEn-Pq1ZiQ0zvDeee4SB0TXBBMBF3XdH1TUEx5gWWBa74CZoSLOtcilKeoinGlOZUlmKCLmLscAJLJs_RhAjKBSn5FMkFDL6HbO77rQ4u-iHzbbaKMFrf-0HHTEMY127wUWdLHdaQrT70GuIlOmv1JsLV8c7Q-9Pj2_w5X74uXuYPy9wwJne5aQBjbStsmagrpmnFBOFtq63UnJSGpb8prbCaWTBQYyqEtW1ZA2kZr2g5Q7cH7zb4zxHiTvUuGths9AB-jEpISTj9B0jqmjMiWALJATTBxxigVdvgeh2-FcFq31V1KnVV-64KS5W6ps3NUT42PdjfxTFkAu4PAKQWXw6CisbBYMC6AGanrHd_6H8Af_GIFg</recordid><startdate>20051202</startdate><enddate>20051202</enddate><creator>Hertveldt, Kirsten</creator><creator>Lavigne, Rob</creator><creator>Pleteneva, Elena</creator><creator>Sernova, Natalia</creator><creator>Kurochkina, Lidia</creator><creator>Korchevskii, Roman</creator><creator>Robben, Johan</creator><creator>Mesyanzhinov, Vadim</creator><creator>Krylov, Victor N.</creator><creator>Volckaert, Guido</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>7QL</scope><scope>7U9</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>H94</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope></search><sort><creationdate>20051202</creationdate><title>Genome Comparison of Pseudomonas aeruginosa Large Phages</title><author>Hertveldt, Kirsten ; Lavigne, Rob ; Pleteneva, Elena ; Sernova, Natalia ; Kurochkina, Lidia ; Korchevskii, Roman ; Robben, Johan ; Mesyanzhinov, Vadim ; Krylov, Victor N. ; Volckaert, Guido</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c448t-cbe00ad70d46974a274615ffad8a513c45ffb3d6da4dece90266ddf39e1f45723</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2005</creationdate><topic>Amino Acid Sequence</topic><topic>bacteriophage genomics</topic><topic>DNA Replication - genetics</topic><topic>Endonucleases - metabolism</topic><topic>Genes, Viral - genetics</topic><topic>Genome, Viral - genetics</topic><topic>homing endonuclease</topic><topic>Inteins</topic><topic>Microscopy, Electron</topic><topic>Molecular Sequence Data</topic><topic>Myoviridae</topic><topic>Myovirus</topic><topic>Open Reading Frames - genetics</topic><topic>phage EL</topic><topic>phage evolution</topic><topic>phage ϕKZ</topic><topic>Pseudomonas aeruginosa</topic><topic>Pseudomonas aeruginosa - ultrastructure</topic><topic>Pseudomonas aeruginosa - virology</topic><topic>Pseudomonas Phages - genetics</topic><topic>Pseudomonas Phages - ultrastructure</topic><topic>Sequence Alignment</topic><topic>Sequence Homology, Amino Acid</topic><topic>Transcription, Genetic - genetics</topic><topic>Viral Proteins - genetics</topic><topic>Virus Activation</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Hertveldt, Kirsten</creatorcontrib><creatorcontrib>Lavigne, Rob</creatorcontrib><creatorcontrib>Pleteneva, Elena</creatorcontrib><creatorcontrib>Sernova, Natalia</creatorcontrib><creatorcontrib>Kurochkina, Lidia</creatorcontrib><creatorcontrib>Korchevskii, Roman</creatorcontrib><creatorcontrib>Robben, Johan</creatorcontrib><creatorcontrib>Mesyanzhinov, Vadim</creatorcontrib><creatorcontrib>Krylov, Victor N.</creatorcontrib><creatorcontrib>Volckaert, Guido</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Virology and AIDS Abstracts</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Journal of molecular biology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Hertveldt, Kirsten</au><au>Lavigne, Rob</au><au>Pleteneva, Elena</au><au>Sernova, Natalia</au><au>Kurochkina, Lidia</au><au>Korchevskii, Roman</au><au>Robben, Johan</au><au>Mesyanzhinov, Vadim</au><au>Krylov, Victor N.</au><au>Volckaert, Guido</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Genome Comparison of Pseudomonas aeruginosa Large Phages</atitle><jtitle>Journal of molecular biology</jtitle><addtitle>J Mol Biol</addtitle><date>2005-12-02</date><risdate>2005</risdate><volume>354</volume><issue>3</issue><spage>536</spage><epage>545</epage><pages>536-545</pages><issn>0022-2836</issn><eissn>1089-8638</eissn><abstract>Pseudomonas aeruginosa phage EL is a dsDNA phage related to the giant ϕKZ-like Myoviridae. The EL genome sequence comprises 211,215
bp and has 201 predicted open reading frames (ORFs). The EL genome does not share DNA sequence homology with other viruses and micro-organisms sequenced to date. However, one-third of the predicted EL gene products (gps) shares similarity (Blast alignments of 17–55% amino acid identity) with ϕKZ proteins. Comparative EL and ϕKZ genomics reveals that these giant phages are an example of substantially diverged genetic mosaics. Based on the position of similar EL and ϕKZ predicted gene products, five genome regions can be delineated in EL, four of which are relatively conserved between EL and ϕKZ. Region IV, a 17.7
kb genome region with 28 predicted ORFs, is unique to EL. Fourteen EL ORFs have been assigned a putative function based on protein similarity. Assigned proteins are involved in DNA replication and nucleotide metabolism (NAD
+-dependent DNA ligase, ribonuclease HI, helicase, thymidylate kinase), host lysis and particle structure. EL-gp146 is the first chaperonin GroEL sequence identified in a viral genome. Besides a putative transposase, EL harbours predicted mobile endonucleases related to H–N–H and LAGLIDADG homing endonucleases associated with group I intron and intein intervening sequences.</abstract><cop>England</cop><pub>Elsevier Ltd</pub><pmid>16256135</pmid><doi>10.1016/j.jmb.2005.08.075</doi><tpages>10</tpages></addata></record> |
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| ispartof | Journal of molecular biology, 2005-12, Vol.354 (3), p.536-545 |
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| subjects | Amino Acid Sequence bacteriophage genomics DNA Replication - genetics Endonucleases - metabolism Genes, Viral - genetics Genome, Viral - genetics homing endonuclease Inteins Microscopy, Electron Molecular Sequence Data Myoviridae Myovirus Open Reading Frames - genetics phage EL phage evolution phage ϕKZ Pseudomonas aeruginosa Pseudomonas aeruginosa - ultrastructure Pseudomonas aeruginosa - virology Pseudomonas Phages - genetics Pseudomonas Phages - ultrastructure Sequence Alignment Sequence Homology, Amino Acid Transcription, Genetic - genetics Viral Proteins - genetics Virus Activation |
| title | Genome Comparison of Pseudomonas aeruginosa Large Phages |
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