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Molecular detection and diversity of novel diterpenoid dioxygenase DitA1 genes from proteobacterial strains and soil samples
Resin acids are tricyclic diterpenoids naturally synthesized by trees that are released from wood during pulping processes. Using a newly designed primer set, genes similar to that encoding the DitA1 catalytic α-subunit of the diterpenoid dioxygenase, a key enzyme in abietane resin acid degradation...
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| Published in: | Environmental microbiology 2007-05, Vol.9 (5), p.1202-1218 |
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| cites | cdi_FETCH-LOGICAL-c4602-16cad4f3504c659eee1464dd007f92962e3e2b528871b7eaaaebe13bd60b30953 |
| container_end_page | 1218 |
| container_issue | 5 |
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| container_title | Environmental microbiology |
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| creator | Witzig, Robert Aly, Hamdy A.H Strömpl, Carsten Wray, Victor Junca, Howard Pieper, Dietmar H |
| description | Resin acids are tricyclic diterpenoids naturally synthesized by trees that are released from wood during pulping processes. Using a newly designed primer set, genes similar to that encoding the DitA1 catalytic α-subunit of the diterpenoid dioxygenase, a key enzyme in abietane resin acid degradation by Pseudomonas abietaniphila BKME-9, could be amplified from different Pseudomonas strains, whereas ditA1 gene sequence types representing distinct branches in the evolutionary tree were amplified from Burkholderia and Cupriavidus isolates. All isolates harbouring a ditA1-homologue were capable of growth on dehydroabietic acid as the sole source of carbon and energy and reverse transcription polymerase chain reaction analysis in three strains confirmed that ditA1 was expressed constitutively or in response to DhA, demonstrating its involvement in DhA-degradation. Evolutionary analyses indicate that gyrB (as a phylogenetic marker) and ditA1 genes have coevolved under purifying selection from their ancestral variants present in the most recent common ancestor of the genera Pseudomonas, Cupriavidus and Burkholderia. A polymerase chain reaction-single-strand conformation poylmorphism fingerprinting method was established to monitor the diversity of ditA1 genes in environmental samples. The molecular fingerprints indicated the presence ofa broad, previously unrecognized diversity of diterpenoid dioxygenase genes in soils, and suggest that other bacterial phyla may also harbour the genetic potential for DhA-degradation. |
| doi_str_mv | 10.1111/j.1462-2920.2007.01242.x |
| format | article |
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Using a newly designed primer set, genes similar to that encoding the DitA1 catalytic α-subunit of the diterpenoid dioxygenase, a key enzyme in abietane resin acid degradation by Pseudomonas abietaniphila BKME-9, could be amplified from different Pseudomonas strains, whereas ditA1 gene sequence types representing distinct branches in the evolutionary tree were amplified from Burkholderia and Cupriavidus isolates. All isolates harbouring a ditA1-homologue were capable of growth on dehydroabietic acid as the sole source of carbon and energy and reverse transcription polymerase chain reaction analysis in three strains confirmed that ditA1 was expressed constitutively or in response to DhA, demonstrating its involvement in DhA-degradation. Evolutionary analyses indicate that gyrB (as a phylogenetic marker) and ditA1 genes have coevolved under purifying selection from their ancestral variants present in the most recent common ancestor of the genera Pseudomonas, Cupriavidus and Burkholderia. A polymerase chain reaction-single-strand conformation poylmorphism fingerprinting method was established to monitor the diversity of ditA1 genes in environmental samples. 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Using a newly designed primer set, genes similar to that encoding the DitA1 catalytic α-subunit of the diterpenoid dioxygenase, a key enzyme in abietane resin acid degradation by Pseudomonas abietaniphila BKME-9, could be amplified from different Pseudomonas strains, whereas ditA1 gene sequence types representing distinct branches in the evolutionary tree were amplified from Burkholderia and Cupriavidus isolates. All isolates harbouring a ditA1-homologue were capable of growth on dehydroabietic acid as the sole source of carbon and energy and reverse transcription polymerase chain reaction analysis in three strains confirmed that ditA1 was expressed constitutively or in response to DhA, demonstrating its involvement in DhA-degradation. Evolutionary analyses indicate that gyrB (as a phylogenetic marker) and ditA1 genes have coevolved under purifying selection from their ancestral variants present in the most recent common ancestor of the genera Pseudomonas, Cupriavidus and Burkholderia. A polymerase chain reaction-single-strand conformation poylmorphism fingerprinting method was established to monitor the diversity of ditA1 genes in environmental samples. The molecular fingerprints indicated the presence ofa broad, previously unrecognized diversity of diterpenoid dioxygenase genes in soils, and suggest that other bacterial phyla may also harbour the genetic potential for DhA-degradation.</description><subject>Bacterial Proteins - classification</subject><subject>Bacterial Proteins - genetics</subject><subject>Burkholderia</subject><subject>Burkholderia - classification</subject><subject>Burkholderia - genetics</subject><subject>Burkholderia - metabolism</subject><subject>Dioxygenases - classification</subject><subject>Dioxygenases - genetics</subject><subject>Diterpenes - metabolism</subject><subject>Diterpenes, Abietane - metabolism</subject><subject>DNA Fingerprinting</subject><subject>Ferredoxins - classification</subject><subject>Ferredoxins - genetics</subject><subject>Molecular Sequence Data</subject><subject>Phylogeny</subject><subject>Proteobacteria - classification</subject><subject>Proteobacteria - genetics</subject><subject>Proteobacteria - physiology</subject><subject>Pseudomonas</subject><subject>Pseudomonas - classification</subject><subject>Pseudomonas - genetics</subject><subject>Pseudomonas - metabolism</subject><subject>Pseudomonas abietaniphila</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><recordid>eNqNUk1v1DAQtRCIfsBfAJ-4Jfgr9ubAoSqlLWqL-Kh6tJxkUnlx4sX2ll2pPx6nWS1H8MXjmffeePyMEKakpHm9X5ZUSFawmpGSEaJKQplg5eYZOtwXnu9jyg7QUYxLQqjiirxEB1QJxSSvDtHjtXfQrp0JuIMEbbJ-xGbscGcfIESbttj3ePQP4HIqQVjB6O1U9pvtPYwmAv5o0wnF-QAR98EPeBV8At-YNuOtcTimYOwYn3SjtzlhhpWD-Aq96I2L8Hq3H6PbT2c_Ti-Kqy_nl6cnV0UrJGEFla3pRM8rIlpZ1QCQBxNdlwfva1ZLBhxYU7HFQtFGgTEGGqC86SRpOKkrfozezbr5Yr_WEJMebGzBOTOCX0etiKhEtZD_BDIiJKe0zsDFDGyDjzFAr1fBDiZsNSV6skgv9fT6enJCTxbpJ4v0JlPf7HqsmwG6v8SdJxnwYQb8tg62_y2sz64vpyjzi5lvY4LNnm_CTy2z_5W-uznXny9uxNe7-pue-r2d8b3x2twHG_Xtd0Yoz-Iq_xjJ_wCnt7nO</recordid><startdate>200705</startdate><enddate>200705</enddate><creator>Witzig, Robert</creator><creator>Aly, Hamdy A.H</creator><creator>Strömpl, Carsten</creator><creator>Wray, Victor</creator><creator>Junca, Howard</creator><creator>Pieper, Dietmar H</creator><general>Oxford, UK : Blackwell Publishing Ltd</general><general>Blackwell Publishing Ltd</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>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope></search><sort><creationdate>200705</creationdate><title>Molecular detection and diversity of novel diterpenoid dioxygenase DitA1 genes from proteobacterial strains and soil samples</title><author>Witzig, Robert ; Aly, Hamdy A.H ; Strömpl, Carsten ; Wray, Victor ; Junca, Howard ; Pieper, Dietmar H</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c4602-16cad4f3504c659eee1464dd007f92962e3e2b528871b7eaaaebe13bd60b30953</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2007</creationdate><topic>Bacterial Proteins - classification</topic><topic>Bacterial Proteins - genetics</topic><topic>Burkholderia</topic><topic>Burkholderia - classification</topic><topic>Burkholderia - genetics</topic><topic>Burkholderia - metabolism</topic><topic>Dioxygenases - classification</topic><topic>Dioxygenases - genetics</topic><topic>Diterpenes - metabolism</topic><topic>Diterpenes, Abietane - metabolism</topic><topic>DNA Fingerprinting</topic><topic>Ferredoxins - classification</topic><topic>Ferredoxins - genetics</topic><topic>Molecular Sequence Data</topic><topic>Phylogeny</topic><topic>Proteobacteria - classification</topic><topic>Proteobacteria - genetics</topic><topic>Proteobacteria - physiology</topic><topic>Pseudomonas</topic><topic>Pseudomonas - classification</topic><topic>Pseudomonas - genetics</topic><topic>Pseudomonas - metabolism</topic><topic>Pseudomonas abietaniphila</topic><topic>Soil Microbiology</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Witzig, Robert</creatorcontrib><creatorcontrib>Aly, Hamdy A.H</creatorcontrib><creatorcontrib>Strömpl, Carsten</creatorcontrib><creatorcontrib>Wray, Victor</creatorcontrib><creatorcontrib>Junca, Howard</creatorcontrib><creatorcontrib>Pieper, Dietmar H</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>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Environmental microbiology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Witzig, Robert</au><au>Aly, Hamdy A.H</au><au>Strömpl, Carsten</au><au>Wray, Victor</au><au>Junca, Howard</au><au>Pieper, Dietmar H</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Molecular detection and diversity of novel diterpenoid dioxygenase DitA1 genes from proteobacterial strains and soil samples</atitle><jtitle>Environmental microbiology</jtitle><addtitle>Environ Microbiol</addtitle><date>2007-05</date><risdate>2007</risdate><volume>9</volume><issue>5</issue><spage>1202</spage><epage>1218</epage><pages>1202-1218</pages><issn>1462-2912</issn><eissn>1462-2920</eissn><notes>http://dx.doi.org/10.1111/j.1462-2920.2007.01242.x</notes><notes>istex:9859EFB0E2EA86FF398D9098AC6DEC2E204EA214</notes><notes>ArticleID:EMI1242</notes><notes>ark:/67375/WNG-JHN4QW9R-5</notes><notes>ObjectType-Article-1</notes><notes>SourceType-Scholarly Journals-1</notes><notes>ObjectType-Feature-2</notes><notes>content type line 23</notes><abstract>Resin acids are tricyclic diterpenoids naturally synthesized by trees that are released from wood during pulping processes. Using a newly designed primer set, genes similar to that encoding the DitA1 catalytic α-subunit of the diterpenoid dioxygenase, a key enzyme in abietane resin acid degradation by Pseudomonas abietaniphila BKME-9, could be amplified from different Pseudomonas strains, whereas ditA1 gene sequence types representing distinct branches in the evolutionary tree were amplified from Burkholderia and Cupriavidus isolates. All isolates harbouring a ditA1-homologue were capable of growth on dehydroabietic acid as the sole source of carbon and energy and reverse transcription polymerase chain reaction analysis in three strains confirmed that ditA1 was expressed constitutively or in response to DhA, demonstrating its involvement in DhA-degradation. Evolutionary analyses indicate that gyrB (as a phylogenetic marker) and ditA1 genes have coevolved under purifying selection from their ancestral variants present in the most recent common ancestor of the genera Pseudomonas, Cupriavidus and Burkholderia. A polymerase chain reaction-single-strand conformation poylmorphism fingerprinting method was established to monitor the diversity of ditA1 genes in environmental samples. The molecular fingerprints indicated the presence ofa broad, previously unrecognized diversity of diterpenoid dioxygenase genes in soils, and suggest that other bacterial phyla may also harbour the genetic potential for DhA-degradation.</abstract><cop>Oxford, UK</cop><pub>Oxford, UK : Blackwell Publishing Ltd</pub><pmid>17472635</pmid><doi>10.1111/j.1462-2920.2007.01242.x</doi><tpages>17</tpages></addata></record> |
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| identifier | ISSN: 1462-2912 |
| ispartof | Environmental microbiology, 2007-05, Vol.9 (5), p.1202-1218 |
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| source | Wiley-Blackwell Journals |
| subjects | Bacterial Proteins - classification Bacterial Proteins - genetics Burkholderia Burkholderia - classification Burkholderia - genetics Burkholderia - metabolism Dioxygenases - classification Dioxygenases - genetics Diterpenes - metabolism Diterpenes, Abietane - metabolism DNA Fingerprinting Ferredoxins - classification Ferredoxins - genetics Molecular Sequence Data Phylogeny Proteobacteria - classification Proteobacteria - genetics Proteobacteria - physiology Pseudomonas Pseudomonas - classification Pseudomonas - genetics Pseudomonas - metabolism Pseudomonas abietaniphila Soil Microbiology |
| title | Molecular detection and diversity of novel diterpenoid dioxygenase DitA1 genes from proteobacterial strains and soil samples |
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