Fluorene degradation by Sphingomonas sp. LB126 proceeds through protocatechuic acid: a genetic analysis

Wattiau, Pierre; Bastiaens, Leen; Herwijnen, R. van; Daal, L.; Parsons, John R.; Renard, Marie Éve; Springael, Dirk; Cornelis, Guy R.

doi:10.1016/s0923-2508(01)01269-4

Cited by 97 publications

(68 citation statements)

References 36 publications

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“…Data used: PmdAB-T2, (this study) PmdAB-BR (AF305325, Providenti et al 2001); ProOab, from Pseudomonas ochraceae (AB127969, Maruyama et al 2004); PcmA, from Arthrobacter keyseri 12B (AF331043, Eaton 2001); FldVU, putative protein from Sphingomonas sp. LB126 (AJ277295, Wattiau et al 2001); Lig AB, from S. paucimobilis SYK-6 (M34835, Noda et al 1990); LigAB-Rp, from Rhodopseudomonas palustris CGA009 (LigA: NP_950035; LigB: NP_950036, Larimer et al 2004) next highest level of identity (28%) is for CarBab, 2-aminobiphenyl-2,3-diol-1,2-dioxygenase of Pseudomonas sp. CA10 (Sato et al 1997).…”

Section: Discussionmentioning

confidence: 99%

Protocatechuate 4,5-dioxygenase from Comamonas testosteroni T-2: biochemical and molecular properties of a new subgroup within class III of extradiol dioxygenases

2005

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Comamonas testosteroni T-2 degraded at least eight aromatic compounds via protocatechuate (PCA), whose extradiol ring cleavage to 2-hydroxy-4-carboxymuconate semialdehyde (HCMS) was catalysed by PCA 4,5-dioxygenase (PmdAB). This inducible, heteromultimeric enzyme was purified. It contained two subunits, a (PmdA) and b (PmdB), and the molecular masses of the denatured proteins were 18 kDa and 31 kDa, respectively. PCA was converted stoichiometrically to HCMS with an apparent K m of 55 lM and at a maximum velocity of 1.5 lkat. Structureactivity-relationship analysis by testing 16 related compounds as substrate for purified PmdAB revealed an absolute requirement for the vicinal diol and for the carboxylate group of PCA. Besides PCA, only 5¢-hydroxy-PCA (gallate) induced oxygen uptake. The Nterminal amino acid sequence of each subunit was identical to the corresponding sequences in C. testosteroni BR6020, which facilitated sequencing of the pmdAB genes in strain T-2. Small differences in the amino acid sequence had significant effects on enzyme stability. Several homologues of pmdAB were found in sequence databases. Residues involved in substrate binding are highly conserved among the homologues. Their sequences grouped within the class III extradiol dioxygenases. Based on our biochemical and genetic analyses, we propose a new branch of the heteromultimeric enzymes within that class.

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Section: Discussionmentioning

confidence: 99%

Protocatechuate 4,5-dioxygenase from Comamonas testosteroni T-2: biochemical and molecular properties of a new subgroup within class III of extradiol dioxygenases

2005

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“…Although these organisms have not been directly tied to nitramine biodegradation, the latter three genera have all been tied to the biodegradation of aromatic compounds. Certain Rhodobacter and Sphingomonas species facilitate ring cleavage via the protocatchuate enzyme whereas certain Methylosinus species can facilitate ring cleavage via a monooxygenase as well as oxidize a variety of aliphatic compounds (Buchan et al, 2001;Wattian et al, 2001;Green and Dalton, 1989). Within the saturated soil, the majority of organisms identified showed traits related to contaminant biodegradation if not specifically nitramine biodegradation.…”

Section: Rdx Biodegradationmentioning

confidence: 99%

Utility of lipid biomarkers in support of bioremediation efforts at army sites

Ringelberg

Richmond

Foley

et al. 2008

Journal of Microbiological Methods

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Lipid biomarker analysis has proven valuable in testing the hypothesis that attributes of the extant microbiota can directly reflect the occurrence of contaminant biodegradation. Two past research efforts have demonstrated this utility and are described here.A 4.5 m vertical core was obtained from a diesel fuel oil contamination plume. Core material was assayed for total petroleum hydrocarbons (TPH) and bacterial membrane phospholipids (PLFA) via a single solvent extraction. Microbial viable biomass and the relative abundance of Gram-negative bacterial PLFA biomarkers were found to be significantly correlated with TPH concentration. The core TPH profile also revealed two distinct areas where the average TPH level of 3000 μg g − 1 fell to near detection limits. Both areas were characterized by a three-fold decrease in the hexadecane/pristane ratio, indicating alkane biodegradation, and a distinct PLFA profile that showed a close similarity to the uncontaminated surface soil. Low-order, incomplete detonations can deposit hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) into training range surface soils. Since surface soils are exposed to temporal and diurnal moisture cycles, we investigated the effect two very different soil moisture tensions had on the in situ microbiota and RDX biodegradation. Saturated soils were characterized by rapid RDX biodegradation, 4 day half-life, a decrease in number of species detected and increase in PLFA biomarkers for Gram-negative proteobacteria (n16:1ω7c, n18:1ω9c, and n18:1ω7c) and Gram-positive firmicutes (i15:0 and a15:0). Terminal restriction fragment length polymorphism (T-RFLP) profiles of endpoint microbial communities indicated a shift from 18 to 36% firmicutes, the loss of gamma-proteobacteria and the emergence of alpha-proteobacteria.These two past research efforts demonstrated the utility of the lipid biomarker analysis in identifying microbial community characteristics that were associated with two very different soil contaminants. Lipid biomarkers defined areas of TPH biodegradation and identified community shifts as a result of soil conditions that affected explosives fate. Information like this can be used to enhance the predictive power of ecological models such as the Army Training and Testing Area Carrying Capacity for munitions model [ATTACC]. Published by Elsevier B.V.

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“…LB126 (Accession No. AJ277295.1 and EU024110.1, respectively; Wattiau et al, 2001;Schuler et al, 2008), suggests the ability of Sphingomonas sp. MCT13 to degrade fluorene.…”

Section: Resultsmentioning

confidence: 99%