Root Nodule
 Bradyrhizobium
 spp. Harbor
 tfdA
 α and
 cadA
 , Homologous with Genes Encoding 2,4-Dichlorophenoxyacetic Acid-Degrading Proteins

Itoh, Kazuhito; Tashiro, Yoshiko; Uobe, Kazuko; Kamagata, Yoichi; Suyama, Kousuke; Yamamoto, Hiroki

doi:10.1128/aem.70.4.2110-2118.2004

Cited by 71 publications

(93 citation statements)

References 46 publications

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“…and Sphingomonas sp. (Itoh et al, 2002(Itoh et al, , 2004Kitagawa et al, 2002). Sphingomonas-and Bradyrhizobium-related PAA degraders are often isolated from soil, are capable of MCPA degradation and Sphingomonas spp.…”

Section: Discussionmentioning

confidence: 99%

“…The first step in the degradation of MCPA is initiated by oxygenases encoded by cadAB or tfdA-like genes (that is, tfdA and tfdAa; Streber et al, 1987;Itoh et al, 2002Itoh et al, , 2004Kitagawa et al, 2002). Such oxygenases cleave the ether-bonded acetate side chain of MCPA to produce 2-methyl-4-chlorophenol (MCP) (Fukumori and Hausinger, 1993a, b;McGowan et al, 1998).…”

Section: Introductionmentioning

confidence: 99%

“…Such oxygenases cleave the ether-bonded acetate side chain of MCPA to produce 2-methyl-4-chlorophenol (MCP) (Fukumori and Hausinger, 1993a, b;McGowan et al, 1998). Major PAAdegrading microorganisms are categorized into three groups on an evolutionary and physiological basis (McGowan et al, 1998;Itoh et al, 2002Itoh et al, , 2004. Group 1 consists of Beta-and Gammaproteobacteria, which harbor tfdA-like genes.…”

Section: Introductionmentioning

confidence: 99%

“…Groups 2 and 3 consist of alphaproteobacterial Bradyrhizobiumand Sphingomonas-related organisms, respectively, including potential novel organisms (Fulthorpe et al, 1995;Kamagata et al, 1997;Zaprasis et al, 2010). Group 2 organisms harbor both tfdA-like and cadA genes, whereas only cadA was detected in group 3 organisms (Itoh et al, 2002(Itoh et al, , 2004Kitagawa et al, 2002;Huong et al, 2007Huong et al, , 2008. As transcription of cadA is induced by 2,4-D in pure cultures, groups 2 and 3 might employ cadA gene homologs for PAA herbicide degradation (Itoh et al, 2002(Itoh et al, , 2004Kitagawa et al, 2002).…”

Section: Introductionmentioning

confidence: 99%

“…Group 2 organisms harbor both tfdA-like and cadA genes, whereas only cadA was detected in group 3 organisms (Itoh et al, 2002(Itoh et al, , 2004Kitagawa et al, 2002;Huong et al, 2007Huong et al, , 2008. As transcription of cadA is induced by 2,4-D in pure cultures, groups 2 and 3 might employ cadA gene homologs for PAA herbicide degradation (Itoh et al, 2002(Itoh et al, , 2004Kitagawa et al, 2002). Diverse and new genes encoding putative PAA oxygenases were recently identified in an agricultural soil (Zaprasis et al, 2010).…”

Section: Introductionmentioning

confidence: 99%

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The earthworm Aporrectodea caliginosa stimulates abundance and activity of phenoxyalkanoic acid herbicide degraders

Zaprasis

Liu

et al. 2010

The ISME Journal

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2-Methyl-4-chlorophenoxyacetic acid (MCPA) is a widely used phenoxyalkanoic acid (PAA) herbicide. Earthworms represent the dominant macrofauna and enhance microbial activities in many soils. Thus, the effect of the model earthworm Aporrectodea caliginosa (Oligochaeta, Lumbricidae) on microbial MCPA degradation was assessed in soil columns with agricultural soil. MCPA degradation was quicker in soil with earthworms than without earthworms. Quantitative PCR was inhibition-corrected per nucleic acid extract and indicated that copy numbers of tfdA-like and cadA genes (both encoding oxygenases initiating aerobic PAA degradation) in soil with earthworms were up to three and four times higher than without earthworms, respectively. tfdA-like and 16S rRNA gene transcript copy numbers in soil with earthworms were two and six times higher than without earthworms, respectively. Most probable numbers (MPNs) of MCPA degraders approximated 4 × 105 gdw−1 in soil before incubation and in soil treated without earthworms, whereas MPNs of earthworm-treated soils were approximately 150 × higher. The aerobic capacity of soil to degrade MCPA was higher in earthworm-treated soils than in earthworm-untreated soils. Burrow walls and 0–5 cm depth bulk soil displayed higher capacities to degrade MCPA than did soil from 5–10 cm depth bulk soil, expression of tfdA-like genes in burrow walls was five times higher than in bulk soil and MCPA degraders were abundant in burrow walls (MPNs of 5 × 107 gdw−1). The collective data indicate that earthworms stimulate abundance and activity of MCPA degraders endogenous to soil by their burrowing activities and might thus be advantageous for enhancing PAA degradation in soil.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

The earthworm Aporrectodea caliginosa stimulates abundance and activity of phenoxyalkanoic acid herbicide degraders

Zaprasis

Liu

et al. 2010

The ISME Journal

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Kinetic Traits and Enzyme Form Patterns of (R)‐2‐(2,4‐Dichlorophenoxy)propionate/α‐Ketoglutarate Dioxygenase (RdpA) after Expression in Different Bacterial Strains

Westendorf

Benndorf

Pribýl

et al. 2006

Engineering in Life Sciences

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The rdpA gene of strains Delftia acidovorans MC1, Rhodoferax sp. P230, and Sphingobium herbicidovorans MH proved to be identical. However, when RdpA [(R)‐2‐(2,4‐dichlorophenoxy)propionate/α‐ketoglutarate dioxygenase] was investigated after purification from the various strains, significant differences in the kinetics and some chemical properties of the enzymes were observed. The preference for substrates ranged in the order (R)‐2‐(2,4‐dichlorophenoxy)propionate (2,4‐DP) > (R)‐2‐(4‐chloro‐2‐methylphenoxy)propionate (MCPP) >> 2,4‐dichlorophenoxyacetate (2,4‐D) ∼ 4‐chloro‐2‐methylphenoxyacetate (MCPA), but detailed kinetic investigations revealed significant strain‐dependent differences in the kcat and KM values. While the KM values of RdpA from the various strains were low and their range rather narrow with 2,4‐DP (19–60 μM) and MCPP (35–64 μM), larger differences were observed with phenoxyacetates which were distinctly higher and spanned a wider range with 2,4‐D (237–935 μM) and MCPA (164–510 μM). The lowest KM values with 2,4‐D and MCPA were found for RdpA originating from strain P230. Investigation of the enzymes from the various sources by 2D gel electrophoresis revealed up to three monomeric enzyme forms which differed in the pI value. The 2D‐patterns were similar with RdpA from strains MC1 and MH, and after heterologous expression of the enzyme in Escherichia coli, but differed significantly from that of strain P230. The presence of enzyme forms and their different composition coincided apparently with the differences observed in the kinetic properties of RdpA in the various strains. The effects are discussed in terms of posttranslational modification of RdpA which appears to be different in extent and kind in the various strains.

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Activity and Reaction Mechanism of the Initial Enzymatic Step Specifying the Microbial Degradation of 2,4‐Dichlorophenoxyacetate

Müller

2007

Engineering in Life Sciences

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The capability of Delftia acidovorans MC1010 (SdpA+, RdpA–) to degrade the herbicides 2,4‐dichlorophenoxyacetate (2,4‐D) and 4‐chloro‐2‐methylphenoxyacetate (MCPA) was investigated in batch degradation experiments and interpreted in the light of the catalytic activity of the initial enzyme SdpA, an α‐ketoglutarate‐dependent dioxygenase, catalyzing the cleavage of the ether bond. Dense inocula of this strain degraded high initial 2,4‐D concentrations quickly to below the detection limit. The specific degradation rate became slower and the degradation remained incomplete when low initial biomass concentrations and/or 2,4‐D concentrations were used. With low initial 2,4‐D concentrations, the degradation rate became nearly concentration‐independent. This effect was less pronounced with MCPA, a substrate that is more readily degraded by SdpA than 2,4‐D. (S)‐2‐(2,4‐dichlorophenoxy)propionate ((S)‐2,4‐DP), the favored substrate of SdpA used as comparison, was almost completely utilized under the various conditions. The observed differences were attributed to the easier regeneration of the essential co‐substrate α‐ketoglutarate with MCPA and above all (S)‐2,4‐DP as a substrate compared to 2,4‐D. Decreasing SdpA activity, which was observed during the starvation of MC1010, will contribute to the apparent recalcitrance of 2,4‐D. Degradation of 2,4‐D by Bradyrhizobium sp. RD5‐C2, a strain initiating 2,4‐D cleavage by a monooxygenase not requiring an organic intermediate as a co‐substrate, proceeded to completion despite the approximately 20‐fold lower degradation rates compared to those obtained with strain MC1010. However, lowering of biomass concentrations resulted in restricted degradation also with strain RD5‐C2. The results were discussed in terms of the kind of co‐substrate in the cleavage reaction, the availability of essential intracellular metabolites, and the cells' maintenance demands.

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Root Nodule Bradyrhizobium spp. Harbor tfdA α and cadA , Homologous with Genes Encoding 2,4-Dichlorophenoxyacetic Acid-Degrading Proteins

Cited by 71 publications

References 46 publications

The earthworm Aporrectodea caliginosa stimulates abundance and activity of phenoxyalkanoic acid herbicide degraders

The earthworm Aporrectodea caliginosa stimulates abundance and activity of phenoxyalkanoic acid herbicide degraders

Kinetic Traits and Enzyme Form Patterns of (R)‐2‐(2,4‐Dichlorophenoxy)propionate/α‐Ketoglutarate Dioxygenase (RdpA) after Expression in Different Bacterial Strains

Activity and Reaction Mechanism of the Initial Enzymatic Step Specifying the Microbial Degradation of 2,4‐Dichlorophenoxyacetate

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