Sequence diversity of the OprD protein of environmental Pseudomonas strains
OprD has been widely described for Pseudomonas aeruginosa at both structural and functional levels. Here, we describe the sequence diversity of the OprD proteins from other fluorescent Pseudomonads. We analysed the sequence of the oprD gene in each of the 49 Pseudomonas isolates, mostly putida and f...
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| Veröffentlicht in: | Environmental microbiology 2007-03, Vol.9 (3), p.824-835 |
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| creator | Chevalier, Sylvie Bodilis, Josselin Jaouen, Thomas Barray, Sylvie Feuilloley, Marc G.J Orange, Nicole |
| description | OprD has been widely described for Pseudomonas aeruginosa at both structural and functional levels. Here, we describe the sequence diversity of the OprD proteins from other fluorescent Pseudomonads. We analysed the sequence of the oprD gene in each of the 49 Pseudomonas isolates, mostly putida and fluorescens species, obtained from various environmental sources, including soil, rhizosphere and hospitals. Phylogeny based on OprD sequences distinguished three well-separated clusters in the P. fluorescens species whereas P. putida isolates formed only one cluster. The OprD sequences were generally well conserved within each cluster whereas on the opposite, they were highly variable from one cluster to another and particularly with regards to the cluster of P. aeruginosa. Predicted secondary structures, based on the topological model elaborated for P. aeruginosa, suggest signatures in the large extracellular loops of OprD, which are linked to the OprD-based clusters. Correlations between these OprD-based clusters and ecological niches, growth on various carbon sources and antibiotic sensitivity were investigated. |
| doi_str_mv | 10.1111/j.1462-2920.2006.01191.x |
| format | Article |
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Here, we describe the sequence diversity of the OprD proteins from other fluorescent Pseudomonads. We analysed the sequence of the oprD gene in each of the 49 Pseudomonas isolates, mostly putida and fluorescens species, obtained from various environmental sources, including soil, rhizosphere and hospitals. Phylogeny based on OprD sequences distinguished three well-separated clusters in the P. fluorescens species whereas P. putida isolates formed only one cluster. The OprD sequences were generally well conserved within each cluster whereas on the opposite, they were highly variable from one cluster to another and particularly with regards to the cluster of P. aeruginosa. Predicted secondary structures, based on the topological model elaborated for P. aeruginosa, suggest signatures in the large extracellular loops of OprD, which are linked to the OprD-based clusters. Correlations between these OprD-based clusters and ecological niches, growth on various carbon sources and antibiotic sensitivity were investigated.</description><identifier>ISSN: 1462-2912</identifier><identifier>EISSN: 1462-2920</identifier><identifier>DOI: 10.1111/j.1462-2920.2006.01191.x</identifier><identifier>PMID: 17298381</identifier><language>eng</language><publisher>Oxford, UK: Oxford, UK : Blackwell Publishing Ltd</publisher><subject>Amino Acid Sequence ; Continental interfaces, environment ; DNA, Bacterial - analysis ; Environmental Microbiology ; Environmental Sciences ; Genetic Variation ; Global Changes ; Hospitals ; Molecular Sequence Data ; Plant Roots - microbiology ; Porins - genetics ; Pseudomonas - classification ; Pseudomonas - genetics ; Pseudomonas - growth & development ; Pseudomonas - isolation & purification ; Pseudomonas aeruginosa ; Pseudomonas aeruginosa - classification ; Pseudomonas aeruginosa - genetics ; Pseudomonas aeruginosa - growth & development ; Pseudomonas aeruginosa - isolation & purification ; Sciences of the Universe ; Sequence Analysis, DNA ; Soil Microbiology</subject><ispartof>Environmental microbiology, 2007-03, Vol.9 (3), p.824-835</ispartof><rights>Distributed under a Creative Commons Attribution 4.0 International License</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c4901-a5aff94e4def33559b55e36291dc88f5e5bc6f68e0c2f146c47045aa6f4807163</citedby><cites>FETCH-LOGICAL-c4901-a5aff94e4def33559b55e36291dc88f5e5bc6f68e0c2f146c47045aa6f4807163</cites><orcidid>0000-0001-6489-438X</orcidid></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.1462-2920.2006.01191.x$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1111%2Fj.1462-2920.2006.01191.x$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>230,314,776,780,881,1411,27901,27902,45550,45551</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/17298381$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://hal.science/hal-00450930$$DView record in HAL$$Hfree_for_read</backlink></links><search><creatorcontrib>Chevalier, Sylvie</creatorcontrib><creatorcontrib>Bodilis, Josselin</creatorcontrib><creatorcontrib>Jaouen, Thomas</creatorcontrib><creatorcontrib>Barray, Sylvie</creatorcontrib><creatorcontrib>Feuilloley, Marc G.J</creatorcontrib><creatorcontrib>Orange, Nicole</creatorcontrib><title>Sequence diversity of the OprD protein of environmental Pseudomonas strains</title><title>Environmental microbiology</title><addtitle>Environ Microbiol</addtitle><description>OprD has been widely described for Pseudomonas aeruginosa at both structural and functional levels. Here, we describe the sequence diversity of the OprD proteins from other fluorescent Pseudomonads. We analysed the sequence of the oprD gene in each of the 49 Pseudomonas isolates, mostly putida and fluorescens species, obtained from various environmental sources, including soil, rhizosphere and hospitals. Phylogeny based on OprD sequences distinguished three well-separated clusters in the P. fluorescens species whereas P. putida isolates formed only one cluster. The OprD sequences were generally well conserved within each cluster whereas on the opposite, they were highly variable from one cluster to another and particularly with regards to the cluster of P. aeruginosa. Predicted secondary structures, based on the topological model elaborated for P. aeruginosa, suggest signatures in the large extracellular loops of OprD, which are linked to the OprD-based clusters. Correlations between these OprD-based clusters and ecological niches, growth on various carbon sources and antibiotic sensitivity were investigated.</description><subject>Amino Acid Sequence</subject><subject>Continental interfaces, environment</subject><subject>DNA, Bacterial - analysis</subject><subject>Environmental Microbiology</subject><subject>Environmental Sciences</subject><subject>Genetic Variation</subject><subject>Global Changes</subject><subject>Hospitals</subject><subject>Molecular Sequence Data</subject><subject>Plant Roots - microbiology</subject><subject>Porins - genetics</subject><subject>Pseudomonas - classification</subject><subject>Pseudomonas - genetics</subject><subject>Pseudomonas - growth & development</subject><subject>Pseudomonas - isolation & purification</subject><subject>Pseudomonas aeruginosa</subject><subject>Pseudomonas aeruginosa - classification</subject><subject>Pseudomonas aeruginosa - genetics</subject><subject>Pseudomonas aeruginosa - growth & development</subject><subject>Pseudomonas aeruginosa - isolation & purification</subject><subject>Sciences of the Universe</subject><subject>Sequence Analysis, DNA</subject><subject>Soil Microbiology</subject><issn>1462-2912</issn><issn>1462-2920</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2007</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqNkU1v1DAQhiMEoqXwFyAnJA4J4zh24gOHqi1txdJCtxXHkTcZUy_5WOzssvvvcchqOYIvtsbPO19vFMUMUhbO-2XKcpklmcogzQBkCowplm6fRMeHj6eHN8uOohfeLwFYwQt4Hh2xIlMlL9lx9GlOP9fUVRTXdkPO22EX9yYeHim-XbnzeOX6gWw3xqjbWNd3LXWDbuIvntZ13_ad9rEfnLadfxk9M7rx9Gp_n0QPHy_uz66S2e3l9dnpLKlyBSzRQhujcsprMpwLoRZCEJehz7oqSyNILCppZElQZSaMUOUF5EJrafISCib5SfRuyvuoG1w522q3w15bvDqd4RiDwIPisGGBfTuxYZAwqB-wtb6iptEd9WuPUgWYCf5PMINcMqnG6uUEVq733pE5tMAAR3dwiePicTQBR3fwjzu4DdLX-xrrRUv1X-HejgB8mIBftqHdfyfGi8_X4yvok0lv_UDbg167HyiD9QK_3VyiKu7ub-6-znGc5c3EG92j_u6sx4d5BowDFLkMW-G_ATcStOw</recordid><startdate>200703</startdate><enddate>200703</enddate><creator>Chevalier, Sylvie</creator><creator>Bodilis, Josselin</creator><creator>Jaouen, Thomas</creator><creator>Barray, Sylvie</creator><creator>Feuilloley, Marc G.J</creator><creator>Orange, Nicole</creator><general>Oxford, UK : Blackwell Publishing Ltd</general><general>Blackwell Publishing Ltd</general><general>Society for Applied Microbiology and Wiley-Blackwell</general><scope>FBQ</scope><scope>BSCLL</scope><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>C1K</scope><scope>7X8</scope><scope>1XC</scope><orcidid>https://orcid.org/0000-0001-6489-438X</orcidid></search><sort><creationdate>200703</creationdate><title>Sequence diversity of the OprD protein of environmental Pseudomonas strains</title><author>Chevalier, Sylvie ; Bodilis, Josselin ; Jaouen, Thomas ; Barray, Sylvie ; Feuilloley, Marc G.J ; Orange, Nicole</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c4901-a5aff94e4def33559b55e36291dc88f5e5bc6f68e0c2f146c47045aa6f4807163</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2007</creationdate><topic>Amino Acid Sequence</topic><topic>Continental interfaces, environment</topic><topic>DNA, Bacterial - analysis</topic><topic>Environmental Microbiology</topic><topic>Environmental Sciences</topic><topic>Genetic Variation</topic><topic>Global Changes</topic><topic>Hospitals</topic><topic>Molecular Sequence Data</topic><topic>Plant Roots - microbiology</topic><topic>Porins - genetics</topic><topic>Pseudomonas - classification</topic><topic>Pseudomonas - genetics</topic><topic>Pseudomonas - growth & development</topic><topic>Pseudomonas - isolation & purification</topic><topic>Pseudomonas aeruginosa</topic><topic>Pseudomonas aeruginosa - classification</topic><topic>Pseudomonas aeruginosa - genetics</topic><topic>Pseudomonas aeruginosa - growth & development</topic><topic>Pseudomonas aeruginosa - isolation & purification</topic><topic>Sciences of the Universe</topic><topic>Sequence Analysis, DNA</topic><topic>Soil Microbiology</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Chevalier, Sylvie</creatorcontrib><creatorcontrib>Bodilis, Josselin</creatorcontrib><creatorcontrib>Jaouen, Thomas</creatorcontrib><creatorcontrib>Barray, Sylvie</creatorcontrib><creatorcontrib>Feuilloley, Marc G.J</creatorcontrib><creatorcontrib>Orange, Nicole</creatorcontrib><collection>AGRIS</collection><collection>Istex</collection><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>Environmental Sciences and Pollution Management</collection><collection>MEDLINE - Academic</collection><collection>Hyper Article en Ligne (HAL)</collection><jtitle>Environmental microbiology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Chevalier, Sylvie</au><au>Bodilis, Josselin</au><au>Jaouen, Thomas</au><au>Barray, Sylvie</au><au>Feuilloley, Marc G.J</au><au>Orange, Nicole</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Sequence diversity of the OprD protein of environmental Pseudomonas strains</atitle><jtitle>Environmental microbiology</jtitle><addtitle>Environ Microbiol</addtitle><date>2007-03</date><risdate>2007</risdate><volume>9</volume><issue>3</issue><spage>824</spage><epage>835</epage><pages>824-835</pages><issn>1462-2912</issn><eissn>1462-2920</eissn><abstract>OprD has been widely described for Pseudomonas aeruginosa at both structural and functional levels. Here, we describe the sequence diversity of the OprD proteins from other fluorescent Pseudomonads. We analysed the sequence of the oprD gene in each of the 49 Pseudomonas isolates, mostly putida and fluorescens species, obtained from various environmental sources, including soil, rhizosphere and hospitals. Phylogeny based on OprD sequences distinguished three well-separated clusters in the P. fluorescens species whereas P. putida isolates formed only one cluster. The OprD sequences were generally well conserved within each cluster whereas on the opposite, they were highly variable from one cluster to another and particularly with regards to the cluster of P. aeruginosa. Predicted secondary structures, based on the topological model elaborated for P. aeruginosa, suggest signatures in the large extracellular loops of OprD, which are linked to the OprD-based clusters. Correlations between these OprD-based clusters and ecological niches, growth on various carbon sources and antibiotic sensitivity were investigated.</abstract><cop>Oxford, UK</cop><pub>Oxford, UK : Blackwell Publishing Ltd</pub><pmid>17298381</pmid><doi>10.1111/j.1462-2920.2006.01191.x</doi><tpages>12</tpages><orcidid>https://orcid.org/0000-0001-6489-438X</orcidid></addata></record> |
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| subjects | Amino Acid Sequence Continental interfaces, environment DNA, Bacterial - analysis Environmental Microbiology Environmental Sciences Genetic Variation Global Changes Hospitals Molecular Sequence Data Plant Roots - microbiology Porins - genetics Pseudomonas - classification Pseudomonas - genetics Pseudomonas - growth & development Pseudomonas - isolation & purification Pseudomonas aeruginosa Pseudomonas aeruginosa - classification Pseudomonas aeruginosa - genetics Pseudomonas aeruginosa - growth & development Pseudomonas aeruginosa - isolation & purification Sciences of the Universe Sequence Analysis, DNA Soil Microbiology |
| title | Sequence diversity of the OprD protein of environmental Pseudomonas strains |
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