Sequence analysis of the 2,4-dichlorophenol hydroxylase gene tfdB and 3,5-dichlorocatechol 1,2-dioxygenase gene tfdC of 2,4-dichlorophenoxyacetic acid degrading plasmid pEST4011

Kõiv, Viia; Marits, Reet; Heinaru, Ain

doi:10.1016/0378-1119(96)00043-1

Cited by 28 publications

(18 citation statements)

References 7 publications

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“…Figure 3 shows the portion of the pEST4011 catabolic region containing the tfd genes, which are organized as follows. There is a cluster of genes comprising tfdC (which codes for 3,5-dichlorocatechol 1,2-dioxygenase) (21), tfdE (which codes for 2-chlorodienelactone hydrolase), tfdB (which codes for 2,4-dichlorophenol hydroxylase), tfdK (which codes for 2,4-D transporter), and tfdA (which codes for 2,4-D/␣-ketoglutarate dioxygenase). tfdR, which encodes a LysR-type transcriptional activator (54), is located immediately upstream and is transcribed divergently from this cluster; almost 2 kb downstream of this cluster lies a gene for (2-chloro)maleylacetate reductase (tfdF); finally, 2,4-dichlorocis,cis-muconate cycloisomerase is encoded by two identical copies of tfdD which are located 2.6 and 9.6 kb upstream of tfdR.…”

Section: Genes Involved In 24-d Degradationmentioning

confidence: 99%

The Completely Sequenced Plasmid pEST4011 Contains a Novel IncP1 Backbone and a Catabolic Transposon Harboring tfd Genes for 2,4-Dichlorophenoxyacetic Acid Degradation

2004

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The herbicide 2,4-dichlorophenoxyacetic acid (2,4-D)-degrading bacterium Achromobacter xylosoxidans subsp. denitrificans strain EST4002 contains plasmid pEST4011. This plasmid ensures its host a stable 2,4-D ؉ phenotype. We determined the complete 76,958-bp nucleotide sequence of pEST4011. This plasmid is a deletion and duplication derivative of pD2M4, the 95-kb highly unstable laboratory ancestor of pEST4011, and was self-generated during different laboratory manipulations performed to increase the stability of the 2,4-D ؉ phenotype of the original strain, strain D2M4(pD2M4). The 47,935-bp catabolic region of pEST4011 forms a transposon-like structure with identical copies of the hybrid insertion element IS1071::IS1471 at the two ends. The catabolic regions of pEST4011 and pJP4, the best-studied 2,4-D-degradative plasmid, both contain homologous, tfd-like genes for complete 2,4-D degradation, but they have little sequence similarity other than that. The backbone genes of pEST4011 are most similar to the corresponding genes of broad-host-range self-transmissible IncP1 plasmids. The backbones of the other three IncP1 catabolic plasmids that have been sequenced (the 2,4-D-degradative plasmid pJP4, the haloacetate-catabolic plasmid pUO1, and the atrazinecatabolic plasmid pADP-1) are nearly identical to the backbone of R751, the archetype plasmid of the IncP1 ␤ subgroup. We show that despite the overall similarity in plasmid organization, the pEST4011 backbone is sufficiently different (51 to 86% amino acid sequence identity between individual backbone genes) from the backbones of members of the three IncP1 subgroups (the ␣, ␤, and ␥ subgroups) that it belongs to a new IncP1subgroup, the ␦ subgroup. This conclusion was also supported by a phylogenetic analysis of the trfA2, korA, and traG gene products of different IncP1 plasmids.Microbial degradation of 2,4-dichlorophenoxyacetic acid (2,4-D), a xenobiotic herbicide used worldwide for almost 60 years, is a well-studied process. Various soil bacteria can use 2,4-D as a carbon and energy source. Therefore, this compound has become a model for studying the evolution and distribution of genes for the degradation of chloroaromatic compounds. A number of bacterial strains belonging to different phylogenetic groups able to mineralize this compound have been found to possess genetically and enzymatically different 2,4-D-catabolic pathways (9,10,(16)(17)(18). The best-studied 2,4-D degradation genes (located in a chromosome or a plasmid) are tfd-like (pJP4-like). The very recently sequenced 87,688-bp plasmid pJP4 (48) from Wautersia eutropha JMP134 (formerly Ralstonia eutropha) was originally isolated in Australia (8), and its tfd genes and the corresponding enzymes responsible for converting 2,4-D to 3-oxoadipate are well characterized (22,23,25,26,35,58). Besides pJP4, there are only two cases in which the DNA regions containing tfd genes for the whole 2,4-D degradation pathway have been sequenced, a chromosomal transposon-like structure (about 30 kb) from Delftia acidovor...

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Section: Genes Involved In 24-d Degradationmentioning

confidence: 99%

The Completely Sequenced Plasmid pEST4011 Contains a Novel IncP1 Backbone and a Catabolic Transposon Harboring tfd Genes for 2,4-Dichlorophenoxyacetic Acid Degradation

2004

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“…The cadABC genes were predicted to encode 2,4-D oxygenase subunits from their deduced amino acid sequences that showed 46, 44, and 37% identities with the TftA and TftB subunits of 2,4,5-trichlorophenoxyacetic acid (2,4,5-T) oxygenase of Burkholderia cepacia AC1100 and with a putative ferredoxin, ThcC, of 2,4-Dichlorophenoxyacetic acid (2,4-D) is a manufactured herbicide that has been widely used for the control of broadleaf weeds since its introduction in the 1940s. Many 2,4-Ddegrading microorganisms have been isolated from agricultural, urban, and industrial soils and sediments (2,3,9,22,30,50), and the catabolic pathway of 2,4-D mineralization in Ralstonia eutropha JMP134 has been extensively characterized (8-10, 14, 19, 25, 26, 32-35, 38, 41-43, 48). In JMP134, 2,4-D is transformed to 2,4-dichlorophenol (2,4-DCP) by ␣-ketoglutarate-dependent 2,4-D dioxygenase encoded by tfdA, and 2,4-DCP is subsequently hydroxylated by 2,4-DCP hydroxylase encoded by tfdB to form 3,5-dichlorocatechol (3,5-DCC).…”

mentioning

confidence: 99%

“…Many 2,4-Ddegrading microorganisms have been isolated from agricultural, urban, and industrial soils and sediments (2,3,9,22,30,50), and the catabolic pathway of 2,4-D mineralization in Ralstonia eutropha JMP134 has been extensively characterized (8-10, 14, 19, 25, 26, 32-35, 38, 41-43, 48). In JMP134, 2,4-D is transformed to 2,4-dichlorophenol (2,4-DCP) by ␣-ketoglutarate-dependent 2,4-D dioxygenase encoded by tfdA, and 2,4-DCP is subsequently hydroxylated by 2,4-DCP hydroxylase encoded by tfdB to form 3,5-dichlorocatechol (3,5-DCC).…”

mentioning

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Novel 2,4-Dichlorophenoxyacetic Acid Degradation Genes from Oligotrophic Bradyrhizobium sp. Strain HW13 Isolated from a Pristine Environment

et al. 2002

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The tfd genes of Ralstonia eutropha JMP134 are the only well-characterized set of genes responsible for 2,4-dichlorophenoxyacetic acid (2,4-D) degradation among 2,4-D-degrading bacteria. A new family of 2,4-D degradation genes, cadRABKC, was cloned and characterized from Bradyrhizobium sp. strain HW13, a strain that was isolated from a buried Hawaiian soil that has never experienced anthropogenic chemicals. The cadR gene was inferred to encode an AraC/XylS type of transcriptional regulator from its deduced amino acid sequence. The cadABC genes were predicted to encode 2,4-D oxygenase subunits from their deduced amino acid sequences that showed 46, 44, and 37% identities with the TftA and TftB subunits of 2,4,5-trichlorophenoxyacetic acid (2,4,5-T) oxygenase of Burkholderia cepacia AC1100 and with a putative ferredoxin, ThcC, of 2,4-Dichlorophenoxyacetic acid (2,4-D) is a manufactured herbicide that has been widely used for the control of broadleaf weeds since its introduction in the 1940s. Many 2,4-Ddegrading microorganisms have been isolated from agricultural, urban, and industrial soils and sediments (2,3,9,22,30,50), and the catabolic pathway of 2,4-D mineralization in Ralstonia eutropha JMP134 has been extensively characterized (8-10, 14, 19, 25, 26, 32-35, 38, 41-43, 48). In JMP134, 2,4-D is transformed to 2,4-dichlorophenol (2,4-DCP) by ␣-ketoglutarate-dependent 2,4-D dioxygenase encoded by tfdA, and 2,4-DCP is subsequently hydroxylated by 2,4-DCP hydroxylase encoded by tfdB to form 3,5-dichlorocatechol (3,5-DCC). 3,5-DCC is further metabolized through an intradiol ring cleavage pathway encoded by tfdCDEF (Fig. 1). These genes are located on plasmid pJP4.Most 2,4-D-degrading bacteria isolated from human-disturbed sites contain tfdA gene homologs. They include various copiotrophic, fast-growing genera in the ␤ and ␥ subdivisions of the Proteobacteria and have been classified as class I 2,4-D degraders (24). Ka et al. reported another group of 2,4-D degraders (class II) that were also isolated from disturbed sites but have neither tfdA gene homologs nor ␣-ketoglutarate-dependent 2,4-D dioxygenase activity (21-23). This group is composed of copiotrophic, fast-growing strains in the ␣ subdivision of the Proteobacteria, mostly belonging to the genus Sphingomonas. Fulthorpe et al. (17) and Kamagata et al. (24) isolated 2,4-D degraders from noncontaminated, pristine soils, degraders which have neither tfdA gene homologs nor ␣-ketoglutarate-dependent 2,4-D dioxygenase activity and, in contrast to those of the other two classes, grow slowly. This group of 2,4-D degraders (class III) is affiliated with the Bradyrhizobium-Agromyces-Nitrobacter-Afipia cluster (A. Saitou, H. Mitsui, and T. Hattori, Abstr. 11th Meet. Jpn. Soc. Microb. Ecol., p. 26, 1995) of oligotrophic bacteria in the ␣ subdivision of the Proteobacteria. The existence of three distinct ecological and genetic classes of 2,4-D degraders indicates a diversity of 2,4-D degradation genes and perhaps of pathways among 2,4-D degraders. However, the 2,4-D ...

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“…11,44,49) , EST4002 23,53) , and TFD44 17,51) ranged from 58 to 68%, except that between the tfdA of strains JMP134 and EST4002, which was 81% (Table 4). These values were calculated using the sequence data in DDBJ (see the footnotes to Table 3 and 4).…”

Section: 4-d-degrading Genes Reported From Strains Jmp134mentioning

confidence: 99%

“…Some of the 2,4-D-degrading betaproteobacteria have DNA fragments whose nucleotide sequences have 95% or more similarity to those of the tfdA, tfdBI, and tfdCI genes of strain JMP134 2,3,33,51) . Other Betaproteobacteria, including Achromobacter xylosoxidans strain EST4002 31) and Burkholderia cepacia strain RASC 45) , have tfdA, tfdB, and tfdC genes whose nucleotide sequences have 90% or more similarity to each other, and 60-80% similarity to those of the tfdA, tfdB I , and tfdC I genes of strain JMP134 3,14,22,23,27,33,41,50,51) . Among 2,4-D-degrading alphaproteobacteria (e.g., Sphingomonas spp.…”

mentioning

confidence: 99%

2,4-Dichrolophenoxyacetic Acid-degrading Genes from Bacteria Isolated from Soil in Japan: Spread of Burkholderia cepacia RASC-type Degrading Genes Harbored on Large Plasmids

et al. 2007

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Fourteen strains of 2,4-dichrolophenoxyacetic acid (2,4-D)-degrading bacteria were isolated from soil samples from eight different sites in Japan and identified as members of the genera Burkholderia, Cupriavidus, and Sphingobium. To characterize them in view of the 2,4-D-degrading genes that they had, the strains were divided into three groups based on similarities of PCR-amplified partial nucleotide sequences of their 2,4-D-degrading genes to the sequences of well-characterized 2,4-D-degrading genes, tfdA, tfdB, and tfdC in Cupriavidus necator strain JMP134, Achromobacter xylosoxidans strain EST4002, and Sphingomonas sp. strain TFD44. The nucleotide sequences of the tfdA, tfdB, and tfdC gene homologs in eight of the 14 strains were highly similar to those in Burkholderia cepacia strain RASC. The eight strains were classified into the RASC subgroup in the EST4002 group. Southern hybridization indicated that at least one set of the putative tfdA, tfdB, and tfdC genes in each of the 14 strains was located on a replicon (ca. 90-600 kb). In particular, the RASC-type 2,4-D-degrading genes of the eight strains were located on plasmids of similar size (ca. 600 kb), and the hybridization experiments suggested that the 2,4-D-degrading genes of seven strains among the eight were located on restriction fragments of the same length. In view of the fact that the seven strains originated from six distant sites in Japan and had different 16S rRNA gene sequences, our results suggest that the RASC-type 2,4-D-degrading genes on similar plasmids were horizontally transferred among bacteria and were distributed throughout Japan.

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Sequence analysis of the 2,4-dichlorophenol hydroxylase gene tfdB and 3,5-dichlorocatechol 1,2-dioxygenase gene tfdC of 2,4-dichlorophenoxyacetic acid degrading plasmid pEST4011

Cited by 28 publications

References 7 publications

The Completely Sequenced Plasmid pEST4011 Contains a Novel IncP1 Backbone and a Catabolic Transposon Harboring tfd Genes for 2,4-Dichlorophenoxyacetic Acid Degradation

The Completely Sequenced Plasmid pEST4011 Contains a Novel IncP1 Backbone and a Catabolic Transposon Harboring tfd Genes for 2,4-Dichlorophenoxyacetic Acid Degradation

Novel 2,4-Dichlorophenoxyacetic Acid Degradation Genes from Oligotrophic Bradyrhizobium sp. Strain HW13 Isolated from a Pristine Environment

2,4-Dichrolophenoxyacetic Acid-degrading Genes from Bacteria Isolated from Soil in Japan: Spread of Burkholderia cepacia RASC-type Degrading Genes Harbored on Large Plasmids

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