Cloning and nucleotide sequence of the 2,3-dihydroxybiphenyl dioxygenase gene from the PCB-degrading strain of Pseudomonas paucimobilis Q1

Taira, Kazunari; Hayase, Nobuki; Arimura, Nariaki; Yamashita, Shigeki; Miyazaki, Toshitsugu; Furukawa, Koichi

doi:10.1021/bi00411a015

Cited by 135 publications

(88 citation statements)

References 20 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Only S. yanoikuyae Q1 gave no product. The sequence of an extradiol dioxygenase of this strain has been determined (Taira et al, 1988). Interestingly, it is most closely related to sequences found in polycyclic aromatic hydrocarbon (PAH) degraders (Hofer et al, 1993).…”

Section: Experimental Evaluation Of the Systemmentioning

confidence: 84%

A genetic system for the rapid isolation of aromatic-ring-hydroxylating dioxygenase activities

Kahl

Höfer

2003

Microbiology

View full text Add to dashboard Cite

Aromatic-ring-hydroxylating dioxygenases (ARHDOs) are key enzymes in the aerobic bacterial metabolism of aromatic compounds. They are of biotechnological importance as they function as biocatalysts in the stereospecific synthesis of chiral synthons and the degradation of aromatic pollutants. This report describes the development and validation of a system for the rapid isolation and characterization of specific ARHDO activities. The system is based on the identification of ARHDO gene segments that encode the enzymes' major functional determinants, on consensus primers for the direct amplification of such partial genes and on a 'recipient' ARHDO gene cluster for the insertion of the amplified segments. Previously, it has been shown that neither the N-nor the C-terminal portions but only the core region of the large or a-subunit of a class II ARHDO significantly influence substrate and product spectra. On the basis of these observations, consensus primers were designed for the amplification of the gene segment encoding the catalytic core of the large subunit. These primers were tested on 11 bacterial isolates known to metabolize aromatic compounds. In 10 cases, a gene fragment of expected length was amplified. DNA sequencing confirmed similarity to ARHDO a-subunit gene cores. The heterologously well-expressible bphA gene cluster of Burkholderia sp. strain LB400 was modified to facilitate the in-frame insertion of amplified segments. It was used successfully to express the resulting hybrid gene clusters and to form catalytically active chimaeric ARHDOs. The metabolic properties of these enzymes differed significantly from each other and from the parental ARHDO of strain LB400. These results indicate that the system described here can be used to rapidly isolate and functionally characterize ARHDO activities, starting from isolated strains, mixtures of organisms or samples of nucleic acids. Applications of the system range from the recruitment of novel ARHDO activities to an improved characterization of natural ARHDO diversity.

show abstract

Section: Experimental Evaluation Of the Systemmentioning

confidence: 84%

A genetic system for the rapid isolation of aromatic-ring-hydroxylating dioxygenase activities

Kahl

Höfer

2003

Microbiology

View full text Add to dashboard Cite

show abstract

“…2). The pahB gene was thought to flank the pahA gene because genes that encode catabolic enzymes are often clustered (13,19,22). We sequenced the nucleotides of a 6-kb region between the EcoRV and Sacl sites (Fig.…”

mentioning

confidence: 99%

Identification and characterization of genes encoding polycyclic aromatic hydrocarbon dioxygenase and polycyclic aromatic hydrocarbon dihydrodiol dehydrogenase in Pseudomonas putida OUS82

et al. 1994

View full text Add to dashboard Cite

Naphthalene and phenanthrene are transformed by enzymes encoded by the pah gene cluster ofPseudomonas putida OUS82. The pahA and pahB genes, which encode the first and second enzymes, dioxygenase and cis-dihydrodiol dehydrogenase, respectively, were identified and sequenced. The DNA sequences showed that pahA and pahB were clustered and that pah/A consisted of four cistrons, pah/Aa paMAb, pahAc, and pahAd, which encode ferredoxin reductase, ferredoxin, and two subunits of the iron-sulfur protein, respectively.Pseudomonas putida OUS82 can assimilate naphthalene and phenanthrene as its sole carbon sources. The strain converts naphthalene and phenanthrene to salicylate and 1-hydroxy-2-naphthoate, respectively, by a shared catabolic pathway (the upper pathway; Fig. 1). Salicylate and 1-hydroxy-2-naphthoate are further degraded by other catabolic enzymes. The enzymes in the upper pathway have broad substrate specificities, and various polycyclic aromatic hydrocarbons other than naphthalene and phenanthrene are oxidized by a high-density suspension of OUS82 cells (9).Previously, we cloned the gene cluster encoding the enzymes of the upper pathway and named it pah (polycyclic aromatic hydrocarbon; 9). The pah region strongly hybridized to a corresponding region of plasmid NAH7 of P. putida G7, which degrades naphthalene (4). All recombinant plasmids carrying pahA have 6.5-and 3.0-kb Sall fragments. The two fragments were seen to be necessary for the dioxygenase phenotype (PahA). A restriction endonuclease map of a region in the fragments resembles that of the nahA region of NAH7 and pDTG1 in P. putida G7 and NCIB 9816-4, which degrade naphthalene (2, 4, 23). The pahA gene was expected to be in that region.Here, we describe the identification and characterization of the pahA and pahB genes, which encode dioxygenase PahA, which is the first enzyme of the pathway and converts polycyclic aromatic hydrocarbon (PAH) to the corresponding cis-dihydrodiol, and dehydrogenase PahB, the second enzyme of the pathway, which converts the product of PahA to the corresponding diol. P. putida OUS8211 (trp-82 Apah-821), a derivative of strain OUS82 that is defective in naphthalene and phenanthrene utilization, and plasmid pDIl, which carries the pahAB gene cluster, were described previously (9). Plasmid NAH7 was described elsewhere (4, 5). Escherichia coli JM109 and plasmid pUC119 were described by Yanisch-Perron et al. (21)

show abstract

“…Although the roles of Sphingomonas are not yet well established, there are reports that the bacteria have the ability to degrade lignin 6,20) and are involved in the pathogenesis of S. paucimobilis 15) .…”

Section: Phylogenetic Characteristicsmentioning

confidence: 99%

Phylogenetic Analysis of Bacterial Populations Found in Groundwater and an Acidic Stream Draining from an Abandoned Coal Mine.

2001

View full text Add to dashboard Cite

A phylogenetic analysis of heterotrophic bacterial populations inhabiting streams and groundwater contaminated by acid mine drainage (AMD) was conducted. The samples were collected from sites around an inactive underground Dae-Sung coal mine at Keumsan, Korea. The investigation showed pigment-forming bacteria to be the major strains inhabiting the pollutant, accounting for up to approximately 50% of all isolates. Twenty-six pigment-forming bacteria were isolated and their taxonomic characteristics determined by phenotypic, chemotaxonomic and phylogenetic analyses. Based on a phylogenetic analysis using 16S ribosomal RNA gene nucleotide sequences, these isolates were found to fall within four major phylogenetic groups: a, b, and g subdivisions of Proteobacteria; and low-G+C gram-positive bacteria. The a-Proteobacteria were further separated into a-1, a-2 and a-4 subclasses. Many isolates from the polluted stream (site P5) and groundwater (site G) were identified as Sphingomonas of the Proteobacteria a-4 subclass. Because strains P5-21 and P5-11 appeared to be novel species within the genus Sphingomonas, the discussion was focused on their taxonomy as well as abundance in the polluted regions.

show abstract

Cloning and nucleotide sequence of the 2,3-dihydroxybiphenyl dioxygenase gene from the PCB-degrading strain of Pseudomonas paucimobilis Q1

Cited by 135 publications

References 20 publications

A genetic system for the rapid isolation of aromatic-ring-hydroxylating dioxygenase activities

A genetic system for the rapid isolation of aromatic-ring-hydroxylating dioxygenase activities

Identification and characterization of genes encoding polycyclic aromatic hydrocarbon dioxygenase and polycyclic aromatic hydrocarbon dihydrodiol dehydrogenase in Pseudomonas putida OUS82

Phylogenetic Analysis of Bacterial Populations Found in Groundwater and an Acidic Stream Draining from an Abandoned Coal Mine.

Contact Info

Product

Resources

About