tfdA
 -Like Genes in 2,4-Dichlorophenoxyacetic Acid-Degrading Bacteria Belonging to the
 Bradyrhizobium-Agromonas-Nitrobacter-Afipia
 Cluster in α-
 Proteobacteria

Itoh, Kazuhito; Kanda, Rie; Sumita, Yoko; Kim, Hongik; Kamagata, Yoichi; Suyama, Kousuke; Yamamoto, Hiroki; Hausinger, Robert P.; Tiedje, James M.

doi:10.1128/aem.68.7.3449-3454.2002

Cited by 80 publications

(95 citation statements)

References 35 publications

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“…However, gene products of tfdA-like genes are capable of PAA conversion (Itoh et al, 2002), indicating a potential role of tfdA-like genes for a (co-metabolic) conversion of MCPA. Indeed, Bradyrhizobium-related tfdA-like genes are abundant in Scheyern soil (Zaprasis et al, 2002(Zaprasis et al, , 2010 and the expression of tfdA-like genes was stimulated by MCPA (Figures 1a and 4a).…”

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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Insight into Soil Organic Pollutants

Mishra

Singla

Singh

et al. 2022

Microbial Biotechnology

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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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tfdA -Like Genes in 2,4-Dichlorophenoxyacetic Acid-Degrading Bacteria Belonging to the Bradyrhizobium-Agromonas-Nitrobacter-Afipia Cluster in α- Proteobacteria

Cited by 80 publications

References 35 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

Insight into Soil Organic Pollutants

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

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