Analysis of the 2,4-dichlorophenoxyacetic acid-degradative plasmid pEST4011 of Achromobacter xylosoxidans subsp. denitrificans strain EST4002

Vedler, Eve; Kõiv, Viia; Heinaru, Ain

doi:10.1016/s0378-1119(00)00329-2

Cited by 48 publications

(33 citation statements)

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“…After maintenance of strain EST4002 on 2,4-D minimal medium agar plates for years, the strain acquired a very stable 2,4-D ϩ phenotype; only 1 to 2% of the cells lost the phenotype when they were grown in Luria-Bertani medium. According to a restriction analysis this strain contained exactly the same pEST4011 plasmid as the 2,4-D ϩ transconjugants of PaW340 (53).…”

Section: Genes Involved In 24-d Degradationmentioning

confidence: 99%

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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%

“…According to hybridization experiments, the tfd-like genes for 2,4-D degradation were all located in pEST4011. 2,4-D Ϫ strain EST4003 (obtained when EST4002 was grown in Luria-Bertani medium) contained plasmid pEST4012 (about 30 kb), from which the whole catabolic region had been deleted (28,53).…”

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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 outgroups were removed afterwards and resulting column gaps were eliminated. References for the published sequences (order as in the alignment): AF130250 (this study); U19883 ; AF169302 (Johnson et al, 2002); NZ_AAAI01000075, Ralstonia metallidurans Reut_75 genome shotgun sequence; AF512952 (Cai & Xun, 2002); NC_003304, positions 2 501 013-2 502 068, Agrobacterium tumefaciens C58 chromosome (Wood et al, 2001); NC_004463, positions 2 938 247-2 939 326, Bradyrhizobium japonicum USDA 110 genome (Kaneko et al, 2002); AJ536297 (Fritsche, 1998); X72850 (Armengaud et al, 1999); U32188 (Vedler et al, 2000); AF030176 (Seibert et al, 1998);M57629 (van der Meer et al, 1991); AF019038 (Kasberg et al, 1997); M35097 (Perkins et al, 1990); AB050198 (Liu et al, 2001); P94135 (Laemmli et al, 2000); NC_004369, positions 3 077 929-3 079 059, Corynebacterium efficiens YS-314 T genome; NC_003450, positions 1 214 871-1 215 941 and 3 257 401-3 258 492, Corynebacterium glutamicum ATCC 13032 T genome; NC_004463, positions 1 096 165-1 097 388, Bradyrhizobium japonicum USDA 110 genome (Kaneko et al, 2002). Fig.…”

Section: Preliminary Characterization Of Orfs Neighbouring the Maleylmentioning

confidence: 99%

Characterization of a gene cluster encoding the maleylacetate reductase from Ralstonia eutropha 335T, an enzyme recruited for growth with 4-fluorobenzoate

et al. 2004

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A gene cluster containing a gene for maleylacetate reductase (EC 1.3.1.32) was cloned from Ralstonia eutropha 335 T (DSM 531 T ), which is able to utilize 4-fluorobenzoate as sole carbon source. Sequencing of this gene cluster showed that the R. eutropha 335 T maleylacetate reductase gene, macA, is part of a novel gene cluster, which is not related to the known maleylacetate-reductase-encoding gene clusters. It otherwise comprises a gene for a hypothetical membrane transport protein, macB, possibly co-transcribed with macA, and a presumed regulatory gene, macR, which is divergently transcribed from macBA. MacA was found to be most closely related to TftE, the maleylacetate reductase from Burkholderia cepacia AC1100 (62 % identical positions) and to a presumed maleylacetate reductase from a dinitrotoluene catabolic gene cluster from B. cepacia R34 (61 % identical positions). By expressing macA in Escherichia coli, it was confirmed that macA encodes a functional maleylacetate reductase. Purification of maleylacetate reductase from 4-fluorobenzoate-grown R. eutropha 335 T cells allowed determination of the N-terminal sequence of the purified protein, which was shown to be identical to that predicted from the cloned macA gene, thus proving that the gene is, in fact, recruited for growth of R. eutropha 335 T with this substrate. INTRODUCTIONMaleylacetate reductases (EC 1.3.1.32) play a crucial role in the aerobic microbial degradation of aromatic compounds. They catalyse the NADH-or NADPH-dependent reduction of maleylacetate or 2-chloromaleylacetate to 3-oxoadipate ( Fig. 1) or of substituted maleylacetates to substituted 3-oxoadipates. In fungi, maleylacetate reductases contribute to the catabolism of very common substrates, such as tyrosine, gentisate, benzoate, 4-hydroxybenzoate, protocatechuate, vanillate, resorcinol and phenol (Karasevich & Ivoilov, 1977;Buswell & Eriksson, 1979;Gaal & Neujahr, 1979;Sparnins et al., 1979;Anderson & Dagley, 1980;Jones et al., 1995). For bacteria, it has been shown that maleylacetate reductases are involved in the degradation of resorcinol and 2,4-dihydroxybenzoate via hydroxyquinol (Larway & Evans, 1965;Chapman & Ribbons, 1976;Stolz & Knackmuss, 1993). Other substrates whose catabolic routes comprise this activity have a more complex structure, such as 2-hydroxydibenzo-p-dioxin and 3-hydroxydibenzofuran (Armengaud et al., 1999), or carry unusual substituents, such as nitro or sulfo groups (Spain & Gibson, 1991;Feigel & Knackmuss, 1993;Jain et al., 1994;Rani & Lalithakumari, 1994), fluorine or chlorine atoms (Duxbury et al., 1970; Schlömann et al., 1990a;Latus et al., 1995;Zaborina et al., 1995;Daubaras et al., 1996;Miyauchi et al., 1999).The maleylacetate reductase genes characterized so far tend to belong to specialized gene clusters for the degradation of aromatic compounds. Thus, 3-hydroxydibenzofuran and 2-hydroxydibenzo-p-dioxin degradation via hydroxyquinol appears to be encoded by a specialized gene cluster comprising most of the genes for the pathway including a maleylac...

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“…The tfdA gene is widely distributed in a range of bacterial strains that belong to the and subdivisions of Proteobacteria. [4][5][6][7][8][9][10][11][12] Strains selected for their capability to utilize racemic phenoxypropionate herbicides like (RS)-2-(2,4-dichlorophenoxy)propionate (2,4-DP, dichlorprop) and (RS)-2-(4-chloro-2-methylphenoxy)propionate (MCPP, mecoprop) are more rare. Examples are Sphingobium herbicidovorans MH, 8,[13][14][15] Delftia acidovorans MC1, 16,17) Rhodoferax sp.…”

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Uptake Kinetics of 2,4-Dichlorophenoxyacetate byDelftia acidovoransMC1 and Derivative Strains: Complex Characteristics in Response to pH and Growth Substrate

Müller

Hoffmann

2006

Bioscience, Biotechnology, and Biochemistry

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Analysis of the 2,4-dichlorophenoxyacetic acid-degradative plasmid pEST4011 of Achromobacter xylosoxidans subsp. denitrificans strain EST4002

Cited by 48 publications

References 33 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

Characterization of a gene cluster encoding the maleylacetate reductase from Ralstonia eutropha 335T, an enzyme recruited for growth with 4-fluorobenzoate

Uptake Kinetics of 2,4-Dichlorophenoxyacetate byDelftia acidovoransMC1 and Derivative Strains: Complex Characteristics in Response to pH and Growth Substrate

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