Genome Integration and Excision by a New Streptomyces Bacteriophage, ϕJoe
Bacteriophages are the source of many valuable tools for molecular biology and genetic manipulation. In , most DNA cloning vectors are based on serine integrase site-specific DNA recombination systems derived from phage. Because of their efficiency and simplicity, serine integrases are also used for...
Gespeichert in:
| Veröffentlicht in: | Applied and environmental microbiology 2017-03, Vol.83 (5) |
|---|---|
| Hauptverfasser: | , , , |
| Format: | Artikel |
| Sprache: | eng |
| Schlagworte: | |
| Online-Zugang: | Volltext |
| Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
| container_end_page | |
|---|---|
| container_issue | 5 |
| container_start_page | |
| container_title | Applied and environmental microbiology |
| container_volume | 83 |
| creator | Fogg, Paul C M Haley, Joshua A Stark, W Marshall Smith, Margaret C M |
| description | Bacteriophages are the source of many valuable tools for molecular biology and genetic manipulation. In
, most DNA cloning vectors are based on serine integrase site-specific DNA recombination systems derived from phage. Because of their efficiency and simplicity, serine integrases are also used for diverse synthetic biology applications. Here, we present the genome of a new
phage, ϕJoe, and investigate the conditions for integration and excision of the ϕJoe genome. ϕJoe belongs to the largest
phage cluster (R4-like) and encodes a serine integrase. The
site from
was used efficiently by an integrating plasmid, pCMF92, constructed using the ϕJoe
locus. The
site for ϕJoe integrase was occupied in several
genomes, including that of
, by a mobile element that varies in gene content and size between host species. Serine integrases require a phage-encoded recombination directionality factor (RDF) to activate the excision reaction. The ϕJoe RDF was identified, and its function was confirmed
Both the integrase and RDF were active in
recombination assays. The ϕJoe site-specific recombination system is likely to be an important addition to the synthetic biology and genome engineering toolbox.
spp. are prolific producers of secondary metabolites, including many clinically useful antibiotics. Bacteriophage-derived integrases are important tools for genetic engineering, as they enable integration of heterologous DNA into the
chromosome with ease and high efficiency. Recently, researchers have been applying phage integrases for a variety of applications in synthetic biology, including rapid assembly of novel combinations of genes, biosensors, and biocomputing. An important requirement for optimal experimental design and predictability when using integrases, however, is the need for multiple enzymes with different specificities for their integration sites. In order to provide a broad platform of integrases, we identified and validated the integrase from a newly isolated
phage, ϕJoe. ϕJoe integrase is active
and
The specific recognition site for integration is present in a wide range of different actinobacteria, including
, an emerging model bacterium in
research. |
| doi_str_mv | 10.1128/AEM.02767-16 |
| format | Article |
| fullrecord | <record><control><sourceid>proquest_pubme</sourceid><recordid>TN_cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_5311408</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>1851696675</sourcerecordid><originalsourceid>FETCH-LOGICAL-c384t-f7d1e8517d741381f62a742dda42a71a6d20ec17b8f1c4f6bb1d8a328e1f9e023</originalsourceid><addsrcrecordid>eNpVkMtOwzAQRS0EouWxY42yZEFgxk4dZ4NUUHmJxwJYW44zKUFNXOwU6IfwXfwSgRYEq5nRHN0ZHcZ2EA4QuTocjq4PgKcyjVGusD5CpuKBEHKV9QGyLOY8gR7bCOEJABKQap31uAIQHKDPLs-ocTVFF01LY2_ayjWRaYpo9Gar8DXk88hEN_Qa3bWepq2r55ZCdGxsS75y00czpv3o4_3S0RZbK80k0PaybrKH09H9yXl8dXt2cTK8iq1QSRuXaYGkBpgWaYJCYSm5SRNeFCbpGjSy4EAW01yVaJNS5jkWygiuCMuMgItNdrTInc7ymgpLTevNRE99VRs_185U-v-mqR712L3ogUBMQHUBe8sA755nFFpdV8HSZGIacrOgsftOZlKmgw7dX6DWuxA8lb9nEPSXft3p19_6NcoO3_372i_841t8AhVRgR8</addsrcrecordid><sourcetype>Open Access Repository</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>1851696675</pqid></control><display><type>article</type><title>Genome Integration and Excision by a New Streptomyces Bacteriophage, ϕJoe</title><source>American Society for Microbiology</source><source>MEDLINE</source><source>PubMed Central</source><source>Alma/SFX Local Collection</source><creator>Fogg, Paul C M ; Haley, Joshua A ; Stark, W Marshall ; Smith, Margaret C M</creator><creatorcontrib>Fogg, Paul C M ; Haley, Joshua A ; Stark, W Marshall ; Smith, Margaret C M</creatorcontrib><description>Bacteriophages are the source of many valuable tools for molecular biology and genetic manipulation. In
, most DNA cloning vectors are based on serine integrase site-specific DNA recombination systems derived from phage. Because of their efficiency and simplicity, serine integrases are also used for diverse synthetic biology applications. Here, we present the genome of a new
phage, ϕJoe, and investigate the conditions for integration and excision of the ϕJoe genome. ϕJoe belongs to the largest
phage cluster (R4-like) and encodes a serine integrase. The
site from
was used efficiently by an integrating plasmid, pCMF92, constructed using the ϕJoe
locus. The
site for ϕJoe integrase was occupied in several
genomes, including that of
, by a mobile element that varies in gene content and size between host species. Serine integrases require a phage-encoded recombination directionality factor (RDF) to activate the excision reaction. The ϕJoe RDF was identified, and its function was confirmed
Both the integrase and RDF were active in
recombination assays. The ϕJoe site-specific recombination system is likely to be an important addition to the synthetic biology and genome engineering toolbox.
spp. are prolific producers of secondary metabolites, including many clinically useful antibiotics. Bacteriophage-derived integrases are important tools for genetic engineering, as they enable integration of heterologous DNA into the
chromosome with ease and high efficiency. Recently, researchers have been applying phage integrases for a variety of applications in synthetic biology, including rapid assembly of novel combinations of genes, biosensors, and biocomputing. An important requirement for optimal experimental design and predictability when using integrases, however, is the need for multiple enzymes with different specificities for their integration sites. In order to provide a broad platform of integrases, we identified and validated the integrase from a newly isolated
phage, ϕJoe. ϕJoe integrase is active
and
The specific recognition site for integration is present in a wide range of different actinobacteria, including
, an emerging model bacterium in
research.</description><identifier>ISSN: 0099-2240</identifier><identifier>EISSN: 1098-5336</identifier><identifier>DOI: 10.1128/AEM.02767-16</identifier><identifier>PMID: 28003200</identifier><language>eng</language><publisher>United States: American Society for Microbiology</publisher><subject>Attachment Sites, Microbiological - genetics ; Bacteriophages - enzymology ; Bacteriophages - genetics ; Bacteriophages - isolation & purification ; Base Sequence ; DNA, Viral ; Escherichia coli - genetics ; Genes, Viral ; Genetic Engineering - methods ; Genetic Vectors ; Genetics and Molecular Biology ; Genome, Viral - genetics ; Integrases - metabolism ; Interspersed Repetitive Sequences - genetics ; Models, Biological ; Plasmids ; Recombination, Genetic ; Sequence Alignment ; Soil Microbiology ; Streptomyces - genetics ; Streptomyces - virology ; Viral Proteins - genetics ; Virus Integration - genetics</subject><ispartof>Applied and environmental microbiology, 2017-03, Vol.83 (5)</ispartof><rights>Copyright © 2017 Fogg et al.</rights><rights>Copyright © 2017 Fogg et al. 2017 Fogg et al.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c384t-f7d1e8517d741381f62a742dda42a71a6d20ec17b8f1c4f6bb1d8a328e1f9e023</citedby><cites>FETCH-LOGICAL-c384t-f7d1e8517d741381f62a742dda42a71a6d20ec17b8f1c4f6bb1d8a328e1f9e023</cites><orcidid>0000-0001-5324-4293 ; 0000-0002-4150-0496</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5311408/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5311408/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,881,3175,27901,27902,53766,53768</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/28003200$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Fogg, Paul C M</creatorcontrib><creatorcontrib>Haley, Joshua A</creatorcontrib><creatorcontrib>Stark, W Marshall</creatorcontrib><creatorcontrib>Smith, Margaret C M</creatorcontrib><title>Genome Integration and Excision by a New Streptomyces Bacteriophage, ϕJoe</title><title>Applied and environmental microbiology</title><addtitle>Appl Environ Microbiol</addtitle><description>Bacteriophages are the source of many valuable tools for molecular biology and genetic manipulation. In
, most DNA cloning vectors are based on serine integrase site-specific DNA recombination systems derived from phage. Because of their efficiency and simplicity, serine integrases are also used for diverse synthetic biology applications. Here, we present the genome of a new
phage, ϕJoe, and investigate the conditions for integration and excision of the ϕJoe genome. ϕJoe belongs to the largest
phage cluster (R4-like) and encodes a serine integrase. The
site from
was used efficiently by an integrating plasmid, pCMF92, constructed using the ϕJoe
locus. The
site for ϕJoe integrase was occupied in several
genomes, including that of
, by a mobile element that varies in gene content and size between host species. Serine integrases require a phage-encoded recombination directionality factor (RDF) to activate the excision reaction. The ϕJoe RDF was identified, and its function was confirmed
Both the integrase and RDF were active in
recombination assays. The ϕJoe site-specific recombination system is likely to be an important addition to the synthetic biology and genome engineering toolbox.
spp. are prolific producers of secondary metabolites, including many clinically useful antibiotics. Bacteriophage-derived integrases are important tools for genetic engineering, as they enable integration of heterologous DNA into the
chromosome with ease and high efficiency. Recently, researchers have been applying phage integrases for a variety of applications in synthetic biology, including rapid assembly of novel combinations of genes, biosensors, and biocomputing. An important requirement for optimal experimental design and predictability when using integrases, however, is the need for multiple enzymes with different specificities for their integration sites. In order to provide a broad platform of integrases, we identified and validated the integrase from a newly isolated
phage, ϕJoe. ϕJoe integrase is active
and
The specific recognition site for integration is present in a wide range of different actinobacteria, including
, an emerging model bacterium in
research.</description><subject>Attachment Sites, Microbiological - genetics</subject><subject>Bacteriophages - enzymology</subject><subject>Bacteriophages - genetics</subject><subject>Bacteriophages - isolation & purification</subject><subject>Base Sequence</subject><subject>DNA, Viral</subject><subject>Escherichia coli - genetics</subject><subject>Genes, Viral</subject><subject>Genetic Engineering - methods</subject><subject>Genetic Vectors</subject><subject>Genetics and Molecular Biology</subject><subject>Genome, Viral - genetics</subject><subject>Integrases - metabolism</subject><subject>Interspersed Repetitive Sequences - genetics</subject><subject>Models, Biological</subject><subject>Plasmids</subject><subject>Recombination, Genetic</subject><subject>Sequence Alignment</subject><subject>Soil Microbiology</subject><subject>Streptomyces - genetics</subject><subject>Streptomyces - virology</subject><subject>Viral Proteins - genetics</subject><subject>Virus Integration - genetics</subject><issn>0099-2240</issn><issn>1098-5336</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2017</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNpVkMtOwzAQRS0EouWxY42yZEFgxk4dZ4NUUHmJxwJYW44zKUFNXOwU6IfwXfwSgRYEq5nRHN0ZHcZ2EA4QuTocjq4PgKcyjVGusD5CpuKBEHKV9QGyLOY8gR7bCOEJABKQap31uAIQHKDPLs-ocTVFF01LY2_ayjWRaYpo9Gar8DXk88hEN_Qa3bWepq2r55ZCdGxsS75y00czpv3o4_3S0RZbK80k0PaybrKH09H9yXl8dXt2cTK8iq1QSRuXaYGkBpgWaYJCYSm5SRNeFCbpGjSy4EAW01yVaJNS5jkWygiuCMuMgItNdrTInc7ymgpLTevNRE99VRs_185U-v-mqR712L3ogUBMQHUBe8sA755nFFpdV8HSZGIacrOgsftOZlKmgw7dX6DWuxA8lb9nEPSXft3p19_6NcoO3_372i_841t8AhVRgR8</recordid><startdate>20170301</startdate><enddate>20170301</enddate><creator>Fogg, Paul C M</creator><creator>Haley, Joshua A</creator><creator>Stark, W Marshall</creator><creator>Smith, Margaret C M</creator><general>American Society for Microbiology</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>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0001-5324-4293</orcidid><orcidid>https://orcid.org/0000-0002-4150-0496</orcidid></search><sort><creationdate>20170301</creationdate><title>Genome Integration and Excision by a New Streptomyces Bacteriophage, ϕJoe</title><author>Fogg, Paul C M ; Haley, Joshua A ; Stark, W Marshall ; Smith, Margaret C M</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c384t-f7d1e8517d741381f62a742dda42a71a6d20ec17b8f1c4f6bb1d8a328e1f9e023</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2017</creationdate><topic>Attachment Sites, Microbiological - genetics</topic><topic>Bacteriophages - enzymology</topic><topic>Bacteriophages - genetics</topic><topic>Bacteriophages - isolation & purification</topic><topic>Base Sequence</topic><topic>DNA, Viral</topic><topic>Escherichia coli - genetics</topic><topic>Genes, Viral</topic><topic>Genetic Engineering - methods</topic><topic>Genetic Vectors</topic><topic>Genetics and Molecular Biology</topic><topic>Genome, Viral - genetics</topic><topic>Integrases - metabolism</topic><topic>Interspersed Repetitive Sequences - genetics</topic><topic>Models, Biological</topic><topic>Plasmids</topic><topic>Recombination, Genetic</topic><topic>Sequence Alignment</topic><topic>Soil Microbiology</topic><topic>Streptomyces - genetics</topic><topic>Streptomyces - virology</topic><topic>Viral Proteins - genetics</topic><topic>Virus Integration - genetics</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Fogg, Paul C M</creatorcontrib><creatorcontrib>Haley, Joshua A</creatorcontrib><creatorcontrib>Stark, W Marshall</creatorcontrib><creatorcontrib>Smith, Margaret C M</creatorcontrib><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>PubMed Central (Full Participant titles)</collection><jtitle>Applied and environmental microbiology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Fogg, Paul C M</au><au>Haley, Joshua A</au><au>Stark, W Marshall</au><au>Smith, Margaret C M</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Genome Integration and Excision by a New Streptomyces Bacteriophage, ϕJoe</atitle><jtitle>Applied and environmental microbiology</jtitle><addtitle>Appl Environ Microbiol</addtitle><date>2017-03-01</date><risdate>2017</risdate><volume>83</volume><issue>5</issue><issn>0099-2240</issn><eissn>1098-5336</eissn><abstract>Bacteriophages are the source of many valuable tools for molecular biology and genetic manipulation. In
, most DNA cloning vectors are based on serine integrase site-specific DNA recombination systems derived from phage. Because of their efficiency and simplicity, serine integrases are also used for diverse synthetic biology applications. Here, we present the genome of a new
phage, ϕJoe, and investigate the conditions for integration and excision of the ϕJoe genome. ϕJoe belongs to the largest
phage cluster (R4-like) and encodes a serine integrase. The
site from
was used efficiently by an integrating plasmid, pCMF92, constructed using the ϕJoe
locus. The
site for ϕJoe integrase was occupied in several
genomes, including that of
, by a mobile element that varies in gene content and size between host species. Serine integrases require a phage-encoded recombination directionality factor (RDF) to activate the excision reaction. The ϕJoe RDF was identified, and its function was confirmed
Both the integrase and RDF were active in
recombination assays. The ϕJoe site-specific recombination system is likely to be an important addition to the synthetic biology and genome engineering toolbox.
spp. are prolific producers of secondary metabolites, including many clinically useful antibiotics. Bacteriophage-derived integrases are important tools for genetic engineering, as they enable integration of heterologous DNA into the
chromosome with ease and high efficiency. Recently, researchers have been applying phage integrases for a variety of applications in synthetic biology, including rapid assembly of novel combinations of genes, biosensors, and biocomputing. An important requirement for optimal experimental design and predictability when using integrases, however, is the need for multiple enzymes with different specificities for their integration sites. In order to provide a broad platform of integrases, we identified and validated the integrase from a newly isolated
phage, ϕJoe. ϕJoe integrase is active
and
The specific recognition site for integration is present in a wide range of different actinobacteria, including
, an emerging model bacterium in
research.</abstract><cop>United States</cop><pub>American Society for Microbiology</pub><pmid>28003200</pmid><doi>10.1128/AEM.02767-16</doi><orcidid>https://orcid.org/0000-0001-5324-4293</orcidid><orcidid>https://orcid.org/0000-0002-4150-0496</orcidid><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 0099-2240 |
| ispartof | Applied and environmental microbiology, 2017-03, Vol.83 (5) |
| issn | 0099-2240 1098-5336 |
| language | eng |
| recordid | cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_5311408 |
| source | American Society for Microbiology; MEDLINE; PubMed Central; Alma/SFX Local Collection |
| subjects | Attachment Sites, Microbiological - genetics Bacteriophages - enzymology Bacteriophages - genetics Bacteriophages - isolation & purification Base Sequence DNA, Viral Escherichia coli - genetics Genes, Viral Genetic Engineering - methods Genetic Vectors Genetics and Molecular Biology Genome, Viral - genetics Integrases - metabolism Interspersed Repetitive Sequences - genetics Models, Biological Plasmids Recombination, Genetic Sequence Alignment Soil Microbiology Streptomyces - genetics Streptomyces - virology Viral Proteins - genetics Virus Integration - genetics |
| title | Genome Integration and Excision by a New Streptomyces Bacteriophage, ϕJoe |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-02-08T02%3A20%3A26IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_pubme&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Genome%20Integration%20and%20Excision%20by%20a%20New%20Streptomyces%20Bacteriophage,%20%CF%95Joe&rft.jtitle=Applied%20and%20environmental%20microbiology&rft.au=Fogg,%20Paul%20C%20M&rft.date=2017-03-01&rft.volume=83&rft.issue=5&rft.issn=0099-2240&rft.eissn=1098-5336&rft_id=info:doi/10.1128/AEM.02767-16&rft_dat=%3Cproquest_pubme%3E1851696675%3C/proquest_pubme%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=1851696675&rft_id=info:pmid/28003200&rfr_iscdi=true |