Characterization of biphenyl dioxygenase sequences and activities encoded by the metagenomes of highly polychlorobiphenyl-contaminated soils.

2.50
Hdl Handle:
http://hdl.handle.net/10033/620826
Title:
Characterization of biphenyl dioxygenase sequences and activities encoded by the metagenomes of highly polychlorobiphenyl-contaminated soils.
Authors:
Standfuss-Gabisch, Christine; Al-Halbouni, Djamila; Hofer, Bernd ( 0000-0002-5174-4021 )
Abstract:
Total extracted DNA from two heavily polychlorobiphenyl-contaminated soils was analyzed with respect to biphenyl dioxygenase sequences and activities. This was done by PCR amplification and cloning of a DNA segment encoding the active site of the enzyme. The translated sequences obtained fell into three similarity clusters (I to III). Sequence identities were high within but moderate or low between the clusters. Members of clusters I and II showed high sequence similarities with well-known biphenyl dioxygenases. Cluster III showed low (43%) sequence identity with a biphenyl dioxygenase from Rhodococcus jostii RHA1. Amplicons from the three clusters were used to reconstitute and express complete biphenyl dioxygenase operons. In most cases, the resulting hybrid dioxygenases were detected in cell extracts of the recombinant hosts. At least 83% of these enzymes were catalytically active. Several amino acid exchanges were identified that critically affected activity. Chlorobiphenyl turnover by the enzymes containing the prototype sequences of clusters I and II was characterized with 10 congeners that were major, minor, or not constituents of the contaminated soils. No direct correlations were observed between on-site concentrations and rates of productive dioxygenations of these chlorobiphenyls. The prototype enzymes displayed markedly different substrate and product ranges. The cluster II dioxygenase possessed a broader substrate spectrum toward the assayed congeners, whereas the cluster I enzyme was superior in the attack of ortho-chlorinated aromatic rings. These results demonstrate the feasibility of the applied approach to functionally characterize dioxygenase activities of soil metagenomes via amplification of incomplete genes.
Affiliation:
Helmholtz Centre for infection research, Inhoffenstr. 7, 38124 Braunschweig, Germany.
Citation:
Characterization of biphenyl dioxygenase sequences and activities encoded by the metagenomes of highly polychlorobiphenyl-contaminated soils. 2012, 78 (8):2706-15 Appl. Environ. Microbiol.
Journal:
Applied and environmental microbiology
Issue Date:
Apr-2012
URI:
http://hdl.handle.net/10033/620826
DOI:
10.1128/AEM.07381-11
PubMed ID:
22327590
Type:
Article
Language:
en
ISSN:
1098-5336
Appears in Collections:
Publications of the research group Chemical Biology (CBIO)

Full metadata record

DC FieldValue Language
dc.contributor.authorStandfuss-Gabisch, Christineen
dc.contributor.authorAl-Halbouni, Djamilaen
dc.contributor.authorHofer, Bernden
dc.date.accessioned2017-02-16T15:16:54Z-
dc.date.available2017-02-16T15:16:54Z-
dc.date.issued2012-04-
dc.identifier.citationCharacterization of biphenyl dioxygenase sequences and activities encoded by the metagenomes of highly polychlorobiphenyl-contaminated soils. 2012, 78 (8):2706-15 Appl. Environ. Microbiol.en
dc.identifier.issn1098-5336-
dc.identifier.pmid22327590-
dc.identifier.doi10.1128/AEM.07381-11-
dc.identifier.urihttp://hdl.handle.net/10033/620826-
dc.description.abstractTotal extracted DNA from two heavily polychlorobiphenyl-contaminated soils was analyzed with respect to biphenyl dioxygenase sequences and activities. This was done by PCR amplification and cloning of a DNA segment encoding the active site of the enzyme. The translated sequences obtained fell into three similarity clusters (I to III). Sequence identities were high within but moderate or low between the clusters. Members of clusters I and II showed high sequence similarities with well-known biphenyl dioxygenases. Cluster III showed low (43%) sequence identity with a biphenyl dioxygenase from Rhodococcus jostii RHA1. Amplicons from the three clusters were used to reconstitute and express complete biphenyl dioxygenase operons. In most cases, the resulting hybrid dioxygenases were detected in cell extracts of the recombinant hosts. At least 83% of these enzymes were catalytically active. Several amino acid exchanges were identified that critically affected activity. Chlorobiphenyl turnover by the enzymes containing the prototype sequences of clusters I and II was characterized with 10 congeners that were major, minor, or not constituents of the contaminated soils. No direct correlations were observed between on-site concentrations and rates of productive dioxygenations of these chlorobiphenyls. The prototype enzymes displayed markedly different substrate and product ranges. The cluster II dioxygenase possessed a broader substrate spectrum toward the assayed congeners, whereas the cluster I enzyme was superior in the attack of ortho-chlorinated aromatic rings. These results demonstrate the feasibility of the applied approach to functionally characterize dioxygenase activities of soil metagenomes via amplification of incomplete genes.en
dc.language.isoenen
dc.rights.urihttp://creativecommons.org/licenses/by-nc-sa/4.0/*
dc.subject.meshCloning, Molecularen
dc.subject.meshCluster Analysisen
dc.subject.meshDioxygenasesen
dc.subject.meshMetagenomeen
dc.subject.meshMolecular Sequence Dataen
dc.subject.meshPhylogenyen
dc.subject.meshPolychlorinated Biphenylsen
dc.subject.meshPolymerase Chain Reactionen
dc.subject.meshSequence Analysis, DNAen
dc.subject.meshSequence Homology, Amino Aciden
dc.subject.meshSoil Microbiologyen
dc.subject.meshSoil Pollutantsen
dc.titleCharacterization of biphenyl dioxygenase sequences and activities encoded by the metagenomes of highly polychlorobiphenyl-contaminated soils.en
dc.typeArticleen
dc.contributor.departmentHelmholtz Centre for infection research, Inhoffenstr. 7, 38124 Braunschweig, Germany.en
dc.identifier.journalApplied and environmental microbiologyen
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