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19F NMR study on the biodegradation of fluorophenols by various Rhodococcus species (1998)

Bondar, Vladimir S. ; Boersma, Marelle G. ; Golovlev, Eugene L. ; [et al.]

Springer

Biodegradation 9 (1998), S. 475-486

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ISSN: 1572-9729

Keywords: biodegradation ; fluorophenols ; 19 F NMR ; oxidative defluorination ; Rhodococcus species

Source: Springer Online Journal Archives 1860-2000

Topics: Biology , Energy, Environment Protection, Nuclear Power Engineering , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition

Notes: Abstract Of all NMR observable isotopes 19F is the one perhaps most convenient for studies on biodegradation of environmental pollutants. The reasons underlying this potential of 19F NMR are discussed and illustrated on the basis of a study on the biodegradation of fluorophenols by four Rhodococcus strains. The results indicate marked differences between the biodegradation pathways of fluorophenols among the various Rhodococcus species. This holds not only for the level and nature of the fluorinated biodegradation pathway intermediates that accumulate, but also for the regioselectivity of the initial hydroxylation step. Several of the Rhodococcus species contain a phenol hydroxylase that catalyses the oxidative defluorination of ortho-fluorinated di- and trifluorophenols. Furthermore, it is illustrated how the 19F NMR technique can be used as a tool in the process of identification of an accumulated unknown metabolite, in this case most likely 5-fluoromaleylacetate. Altogether, the 19F NMR technique proved valid to obtain detailed information on the microbial biodegradation pathways of fluorinated organics, but also to provide information on the specificity of enzymes generally considered unstable and, for this reason, not much studied so far.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1023/A:1008391906885

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2

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Biological, thermal and photochemical transformation of 2-trifluoromethylphenol (1998)

Reinscheid, Uwe Michael ; Zuilhof, Han ; Müller, Rudolf ; [et al.]

Springer

Biodegradation 9 (1998), S. 487-499

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ISSN: 1572-9729

Keywords: Bacillus ; biotransformation ; NMR ; thermophilic ; trifluoromethylphenol

Source: Springer Online Journal Archives 1860-2000

Topics: Biology , Energy, Environment Protection, Nuclear Power Engineering , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition

Notes: Abstract This is the first report on the metabolism of trifluoromethyl aromatics in a thermophilic bacterium, Bacillus thermoleovorans A2. Enzymes of the phenol degradation pathway are induced when cultivating Bacillus thermoleovorans A2 on complex medium. Direct measurements of fluorinated xenobiotics in cell suspensions using 19F-NMR made it possible to follow quantitatively the biotransformation routes. During the biotransformation of 2-CF3-phenol by B. thermoleovorans A2, a fluorinated metabolite, 2-hydroxy-6-oxo-7,7,7,-trifluorohepta-2,4-dienoate (7-TFHOD), accumulated. This metabolite is transformed non-enzymatically when exposed to sunlight. The accumulation of 7-TFHOD as an intermediate in the 2-CF3-phenol pathway was rationalized by calculating molecular properties of a series of meta-cleavage products.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1023/A:1008394115008

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3

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Computer calculation-based quantitative structure-activity relationships for the oxidation of phenol derivatives horseradish peroxidase compound II (1996)

van Haandel, Marjon J. H. ; Rietjens, I. M. C. M. ; Soffers, Ans E. M. F. ; [et al.]

Springer

JBIC 1 (1996), S. 460-467

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ISSN: 1432-1327

Keywords: Key words QSAR ; Horseradish peroxidase ; Compound II ; Phenol derivatives

Source: Springer Online Journal Archives 1860-2000

Topics: Biology , Chemistry and Pharmacology

Notes: Abstract The second-order rate constants for the oxidation of a series of phenol derivatives by horseradish peroxidase compound II were compared to computer-calculated chemical parameters characteristic for this reaction step. The phenol derivatives studied were phenol, 4-chlorophenol, 3-hydroxyphenol, 3-methylphenol, 4-methylphenol, 4-hydroxybenzoate, 4-methoxyphenol and 4-hydroxybenzaldehyde. Assuming a reaction of the phenolic substrates in their non-dissociated, uncharged forms, clear correlations (r = 0.977 and r = 0.905) were obtained between the natural logarithm of the second-order rate constants (ln k app and ln k 2 respectively) for their oxidation by compound II and their calculated ionisation potential, i.e. minus the energy of their highest occupied molecular orbital [E(HOMO)]. In addition to this first approach in which the quantitative structure-activity relationship (QSAR) was based on a calculated frontier orbital parameter of the substrate, in a second and third approach the relative heat of formation (ΔΔHF) calculated for the process of one-electron abstraction and H• abstraction from the phenol derivatives was used as a parameter. Plots of the natural logarithms of the second-order rate constants (k app and k 2) for the reaction and the calculated ΔΔHF values for the process of one-electron abstraction also provide clear QSARs with correlation coefficients of –0.968 and –0.926 respectively. Plots of the natural logarithms of the second-order rate constants (k app and k 2) for the reaction and the calculated ΔΔHF values for the process of H• abstraction provide QSARs with correlation coefficients of –0.989 and –0.922 respectively. Since both mechanisms considered, i.e. initial electron abstraction versus initial H• abstraction, provided clear QSARs, the results could not be used to discriminate between these two possible mechanisms for phenol oxidation by horseradish peroxidase compound II. The computer calculation-based QSARs thus obtained for the oxidation of the various phenol derivatives by compound II from horseradish peroxidase indicate the validity of the approaches investigated, i.e. both the frontier orbital approach and the approach in which the process is described by calculated relative heats of formation. The results also indicate that outcomes from computer calculations on relatively unrelated phenol derivatives can be reliably compared to one another. Furthermore, as the actual oxidation of peroxidase substrates by compound II is known to be the rate-limiting step in the overall catalysis by horseradish peroxidase, the QSARs of the present study may have implications for the differences in the overall rate of substrate oxidation of the phenol derivatives by horseradish peroxidase.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1007/s007750050079

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4

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Possible role of a short extra loop of the long-chain flavodoxin from Azotobacter chroococcum in electron transfer to nitrogenase: Complete 1H, 15N and 13C backbone assignments and secondary solution structure of the flavodoxin (1996)

Peelen, Sjaak ; Wijmenga, Sybren S. ; Erbel, Paul J. A. ; [et al.]

Springer

Journal of biomolecular NMR 7 (1996), S. 315-330

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ISSN: 1573-5001

Keywords: Triple-resonance 3D NMR ; Resonance assignments ; Chemical shifts ; Protein secondary structure ; Electron transfer ; Nitrogen fixation

Source: Springer Online Journal Archives 1860-2000

Topics: Biology , Chemistry and Pharmacology

Notes: Summary The 1H, 15N and 13C backbone and 1H and 13C beta resonance assignments of the long-chain flavodoxin from Azotobacter chroococcum (the 20-kDa nifF product, flavodoxin-2) in its oxidized form were made at pH 6.5 and 30°C using heteronuclear multidimensional NMR spectroscopy. Analysis of the NOE connectivities, together with amide exchange rates, 3JHnHα coupling constants and secondary chemical shifts, provided extensive solution secondary structure information. The secondary structure consists of a five-stranded parallel β-sheet and five α-helices. One of the outer regions of the β-sheet shows no regular extended conformation, whereas the outer strand β4/6 is interrupted by a loop, which is typically observed in long-chain flavodoxins. Two of the five α-helices are nonregular at the N-terminus of the helix. Loop regions close to the FMN are identified. Negatively charged amino acid residues are found to be mainly clustered around the FMN, whereas a cluster of positively charged residues is located in one of the α-helices. Titration of the flavodoxin with the Fe protein of the A. chroococcum nitrogenase enzyme complex revealed that residues Asn11, Ser68 and Asn72 are involved in complex formation between the flavodoxin and Fe protein. The interaction between the flavodoxin and the Fe protein is influenced by MgADP and is of electrostatic nature.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1007/BF00200433

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5

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Molecular characerization of the interaction between the fungal pathogen Cladosporium fulvum and tomato (1994)

Honée, Guy ; Ackerveken, Guido F. J. M. ; Broek, Henk W. J. ; [et al.]

Springer

Euphytica 79 (1994), S. 219-225

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ISSN: 1573-5060

Keywords: Avirulence ; defense response ; high affinity binding sites ; pathogenicity ; race specific elicitor ; structure-function analysis ; transgenic plants

Source: Springer Online Journal Archives 1860-2000

Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition

Notes: Abstract The fungus Cladosprium fulvum is a biotrophic leaf pathogen of tomato. The fungus develops in the intercellular space without forming specialized feeding structures and does not affect the leaf tissue. The outcome of the C. fulvum-tomato interaction can be described by the gene-for-gene model. Failure of infection is expressed by a hypersensitive response. Two fungal proteins, ECP1 and ECP2, have been isolated and their corresponding genes have been cloned. In a compatible interaction including many physiological races ECP1 and ECP2 are highly produced and a role in pathogenicity is suggestive. The ecp1 gene shows some homology with tumor necrosis factor receptors (TNFRs) while the ecp2 gene shows no homology with sequences known in data bases. However, disruption of one of the two genes showed no reduced pathogenicity of the fungus. Two race-specific elicitors, AVR4 and AVR9, have been isolated and their corresponding genes have been cloned. The avirulence genes Avr4 and Avr9 are only present in C. fulvum avirulent on Cf-4 and Cf-9 cultivars, respectively. The expression of these two genes is, like the expression of the ecp genes, highly induced when the fungus grows in planta. Disruption of the Avr9 gene in wild type avirulent races leads to virulence on tomato genotypes carrying the complementary resistance gene Cf-9. A single base-pair change in the avirulence gene Avr4 leads to virulence on tomato genotypes carrying the Cf-4 resistance gene. Isolation, characterization and possible function of ECP1, ECP2, AVR4, and AVR9 will be discussed.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1007/BF00022522

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6

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Molecular and biochemical basis of the interaction between tomato and its fungal pathogen Cladosporium fulvum (1997)

de Wit, Pierre J.G.M. ; Laugé, Richard ; Honée, Guy ; [et al.]

Springer

Antonie van Leeuwenhoek 71 (1997), S. 137-141

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ISSN: 1572-9699

Keywords: avirulence genes ; defence responses ; gene-for-gene ; resistance gene ; specific elicitor ; virulence ; hypersensitive response ; signal transduction

Source: Springer Online Journal Archives 1860-2000

Topics: Biology

Notes: Abstract The interaction between the biotrophic fungal pathogen Cladosporium fulvum and tomato complies with the genefor-gene model. Resistance, expressed as a hypersensitive response (HR) followed by other defence responses, is based on recognition of products of avirulence genes from C. fulvum (race-specific elicitors) by receptors (putative products of resistance genes) in the host plant tomato. The AVR9 elicitor is a 28 amino acid (aa) peptide and the AVR4 elicitor a 106 aa peptide which both induce HR in tomato plants carrying the complementary resistance genes Cf9 and Cf4, respectively. The 3-D structure of the AVR9 peptide, as determined by 1H NMR, revealed that AVR9 belongs to a family of peptides with a cystine knot motif. This motif occurs in channel blockers, peptidase inhibitors and growth factors. The Cf9 resistance gene encodes a membrane-anchored extracellular glycoprotein which contains leucine-rich repeats (LRRs). 125I labeled AVR9 peptide shows the same affinity for plasma membranes of Cf9+ and Cf9- tomato leaves. Membranes of solanaceous plants tested so far all contain homologs of the Cf9 gene and show similar affinities for AVR9. It is assumed that for induction of HR, at least two plant proteins (presumably CF9 and one of his homologs) interact directly or indirectly with the AVR9 peptide which possibly initiates modulation and dimerisation of the receptor, and activation of various other proteins involved in downstream events eventually leading to HR. We have created several mutants of the Avr9 gene, expressed them in the potato virus X (PVX) expression system and tested their biological activity on Cf9 genotypes of tomato. A positive correlation was observed between the biological activity of the mutant AVR9 peptides and their affinity for tomato plasma membranes. Recent results on structure and biological activity of AVR4 peptides encoded by avirulent and virulent alleles of the Avr4 gene (based on expression studies in PVX) are also discussed as well as early defence responses induced by elicitors in tomato leaves and tomato cell suspensions.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1023/A:1000102509556

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