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1.
J Virol Methods ; 329: 114987, 2024 Jun 18.
Article in English | MEDLINE | ID: mdl-38901647

ABSTRACT

One-step RT-qPCR TaqMan assays have been developed for six plant viruses with considerable economic impact in the growing of tulip and lily bulbs: lily mottle virus, lily symptomless virus, lily virus X, Plantago asiatica mosaic virus, tulip breaking virus and tulip virus X. To enhance efficacy and cost-efficiency these assays were combined into multiplex panels. Four different multiplex panels were designed, each consisting of three virus assays and an adapted assay for the housekeeping gene nad5 of lilies and tulips, that acts as an internal amplification control. To eliminate false negative results due to variation in the viral genome sequences, for each target virus two assays were developed on distinct conserved genomic regions. Specificity, PCR efficiency and compatibility of primers and probes were tested using gBlock constructions. Diagnostic samples were used to evaluate the strategy. High Throughput Sequencing of a set of the diagnostic samples, further verified the presence or absence of the viruses in the RNA samples and sequence variations in the target genes. This interchangeable multiplex panel strategy may be a valuable tool for the detection of viruses in certification, surveys and virus diagnostics.

2.
Phytopathology ; 103(11): 1169-79, 2013 Nov.
Article in English | MEDLINE | ID: mdl-23777407

ABSTRACT

The obligate biotrophic pathogen Puccinia horiana is the causal agent of chrysanthemum white rust. Although P. horiana is a quarantine organism, it has been able to spread to most chrysanthemum-producing regions in the world since the 1960s; however, the transfer routes are largely obscure. An extremely low level of allelic diversity was observed in a geographically diverse set of eight isolates using complexity reduction of polymorphic sequences (CRoPS) technology. Only 184 of the 16,196 contigs (1.1%) showed one or more single-nucleotide polymorphisms (SNPs). Thirty-two SNPs and one simple-sequence repeat were translated into molecular markers and used to genotype 45 isolates originating from North and South America, Asia, and Europe. In most cases, phylogenetic clustering was related to geographic origin, indicating local establishment. The European isolates mostly grouped in two major populations that may relate to the two historic introductions previously reported. However, evidence of recent geographic transfer was also observed, including transfer events between Europe and South America and between Southeast Asia and Europe. In contrast with the presumed clonal propagation of this microcyclic rust, strong indications of marker recombination were observed, presumably as a result of anastomosis, karyogamy, and somatic meiosis. Recombination and transfer also explain the geographic dispersal of specific markers. A near-to-significant correlation between the genotypic data and previously obtained pathotype data was observed and one marker was associated with the most virulent pathotype group. In combination with a fast SNP detection method, the markers presented here will be helpful tools to further elucidate the transfer pathways and local survival of this pathogen.


Subject(s)
Basidiomycota/genetics , Chrysanthemum/microbiology , Genetic Variation , Plant Diseases/microbiology , Recombination, Genetic , Amplified Fragment Length Polymorphism Analysis , Asia , Base Sequence , Basidiomycota/classification , Basidiomycota/isolation & purification , DNA, Fungal/chemistry , DNA, Fungal/genetics , Europe , Genetic Markers/genetics , Genotype , Molecular Sequence Data , North America , Phylogeny , Polymorphism, Single Nucleotide , Sequence Analysis, DNA , South America
3.
Lett Appl Microbiol ; 55(5): 390-6, 2012 Nov.
Article in English | MEDLINE | ID: mdl-25998830

ABSTRACT

AIMS: To evaluate the accuracy of pyrosequencing for the description of Phytophthora communities in terms of taxa identification and risk of assignment for false Molecular Operational Taxonomic Units (MOTUs). METHODS AND RESULTS: Pyrosequencing of Internal Transcribed Spacer 1 (ITS1) amplicons was used to describe the structure of a DNA mixture comprising eight Phytophthora spp. and Pythium vexans. Pyrosequencing resulted in 16 965 reads, detecting all species in the template DNA mixture. Reducing the ITS1 sequence identity threshold resulted in a decrease in numbers of unmatched reads but a concomitant increase in the numbers of false MOTUs. The total error rate was 0·63% and comprised mainly mismatches (0·25%) CONCLUSIONS: Pyrosequencing of ITS1 region is an efficient and accurate technique for the detection and identification of Phytophthora spp. in environmental samples. However, the risk of allocating false MOTUs, even when demonstrated to be low, may require additional validation with alternative detection methods. SIGNIFICANCE AND IMPACT OF THE STUDY: Phytophthora spp. are considered among the most destructive groups of invasive plant pathogens, affecting thousands of cultivated and wild plants worldwide. Simultaneous early detection of Phytophthora complexes in environmental samples offers an unique opportunity for the interception of known and unknown species along pathways of introduction, along with the identification of these organisms in invaded environments.


Subject(s)
DNA, Ribosomal Spacer/genetics , Phytophthora/classification , Pythium/classification , Pythium/genetics , Bacterial Typing Techniques , Base Sequence , Mycelium/growth & development , Phytophthora/genetics , Phytophthora/isolation & purification , Plant Diseases/microbiology , Plants/microbiology , Pythium/isolation & purification , Sequence Analysis, DNA/methods
4.
Mol Ecol ; 19(1): 92-107, 2010 Jan.
Article in English | MEDLINE | ID: mdl-20002581

ABSTRACT

Co-existence of both mating types A1 and A2 within the EU1 lineage of Phytophthora ramorum has only been observed in Belgium, which begs the question whether sexual reproduction is occurring. A collection of 411 Belgian P. ramorum isolates was established during a 7-year survey. Our main objectives were genetic characterization of this population to test for sexual reproduction, determination of population structure, evolution and spread, and evaluation of the effectiveness and impact of control measures. Novel, polymorphic simple sequence repeat (SSR) markers were developed after screening 149 candidate loci. Eighty isolates of P. ramorum, broadly representing the Belgian population, were analyzed using four previously described and three newly identified polymorphic microsatellite loci as well as amplified fragment length polymorphisms. SSR analysis was most informative and was used to screen the entire Belgian population. Thirty multilocus genotypes were identified, but 68% of the isolates belonged to the main genotype EU1MG1. Although accumulated mutation events were detected, the overall level of genetic diversity within the Belgian isolates of P. ramorum appears to be limited, indicating a relatively recent clonal expansion. Based on our SSR analysis there is no evidence of sexual recombination in the Belgian population of P. ramorum. Metalaxyl use decreased the genetic diversity of P. ramorum until 2005, when the majority of the isolates had become resistant. Most genotypes were site-specific and despite systematic removal of symptomatic and neighbouring plants, some genotypes were detected over a period of several years at a single site, sometimes discontinuously, indicating (latent) survival of the pathogen at those sites.


Subject(s)
Evolution, Molecular , Genetics, Population , Microsatellite Repeats , Phytophthora/genetics , Alanine/analogs & derivatives , Alanine/pharmacology , Amplified Fragment Length Polymorphism Analysis , Belgium , DNA, Fungal/genetics , Fungicides, Industrial/pharmacology , Genetic Markers , Genotype , Geography , Phytophthora/classification , Phytophthora/drug effects , Recombination, Genetic , Sequence Analysis, DNA
5.
Appl Environ Microbiol ; 75(12): 4185-93, 2009 Jun.
Article in English | MEDLINE | ID: mdl-19395562

ABSTRACT

Simultaneous detection and identification of multiple pathogenic microorganisms in complex environmental samples are required in numerous diagnostic fields. Here, we describe the development of a novel, background-free ligation detection (LD) system using a single compound detector probe per target. The detector probes used, referred to as padlock probes (PLPs), are long oligonucleotides containing asymmetric target complementary regions at both their 5' and 3' ends which confer extremely specific target detection. Probes also incorporate a desthiobiotin moiety and an internal endonuclease IV cleavage site. DNA samples are PCR amplified, and the resulting products serve as potential targets for PLP ligation. Upon perfect target hybridization, the PLPs are circularized via enzymatic ligation, captured, and cleaved, allowing only the originally ligated PLPs to be visualized on a universal microarray. Unlike previous procedures, the probes themselves are not amplified, thereby allowing a simple PLP cleavage to yield a background-free assay. We designed and tested nine PLPs targeting several oomycetes and fungi. All of the probes specifically detected their corresponding targets and provided perfect discrimination against closely related nontarget organisms, yielding an assay sensitivity of 1 pg genomic DNA and a dynamic detection range of 10(4). A practical demonstration with samples collected from horticultural water circulation systems was performed to test the robustness of the newly developed multiplex assay. This novel LD system enables highly specific detection and identification of multiple pathogens over a wide range of target concentrations and should be easily adaptable to a variety of applications in environmental microbiology.


Subject(s)
DNA, Fungal/genetics , Environmental Microbiology , Fungi/classification , Fungi/isolation & purification , Molecular Diagnostic Techniques/methods , Oomycetes/classification , Oomycetes/isolation & purification , Animals , Fungi/genetics , Nucleic Acid Hybridization/methods , Oomycetes/genetics , Polymerase Chain Reaction/methods , Sensitivity and Specificity
6.
Phytopathology ; 97(9): 1119-29, 2007 Sep.
Article in English | MEDLINE | ID: mdl-18944177

ABSTRACT

ABSTRACT In this study, six methods for the detection of Phytophthora ramorum in planta were compared using naturally infested rhododendron plant material. The methods included two immunological methods, one an enzyme-linked immunosorbent assay (ELISA) and the other using a lateral flow format (LFD). Three molecular tests based on the polymerase chain reaction (PCR) using TaqMan chemistry also were assessed, including two assays designed for specific detection of P. ramorum and one designed for genus-level detection of Phytophthora. Isolation followed by morphological identification also was assessed. The diagnostic values of each of the methods, evaluated based on diagnostic sensitivity, diagnostic specificity, positive predictive value, and negative predictive value, were calculated based upon the test results from 148 field samples. The "gold standard" used for the calculations was the final diagnosis, which was based on either a positive PCR result or successful isolation of P. ramorum. The Phytophthora spp. TaqMan PCR, ELISA, and LFD had higher sensitivities than the P. ramorum-specific methods, which make them useful as prescreening methods, where positive results must be confirmed by PCR or isolation. The article discusses practical advantages and disadvantages of each of the methods and how they are valuable in the diagnostic process, according to the circumstances of use (that is, diagnosis or surveillance) and in relation to the prevalence of P. ramorum infestation in the population to be tested.

7.
Mol Ecol ; 15(6): 1493-505, 2006 May.
Article in English | MEDLINE | ID: mdl-16629806

ABSTRACT

Analysis of 12 polymorphic simple sequence repeats identified in the genome sequence of Phytophthora ramorum, causal agent of 'sudden oak death', revealed genotypic diversity to be significantly higher in nurseries (91% of total) than in forests (18% of total). Our analysis identified only two closely related genotypes in US forests, while the genetic structure of populations from European nurseries was of intermediate complexity, including multiple, closely related genotypes. Multilocus analysis determined populations in US forests reproduce clonally and are likely descendants of a single introduced individual. The 151 isolates analysed clustered in three clades. US forest and European nursery isolates clustered into two distinct clades, while one isolate from a US nursery belonged to a third novel clade. The combined microsatellite, sequencing and morphological analyses suggest the three clades represent distinct evolutionary lineages. All three clades were identified in some US nurseries, emphasizing the role of commercial plant trade in the movement of this pathogen.


Subject(s)
Microsatellite Repeats , Phytophthora/genetics , Trees , Europe , Gene Frequency , Genetic Markers , Phylogeny , Phytophthora/classification , Polymorphism, Genetic , Sequence Analysis, DNA , United States
8.
Fungal Genet Biol ; 41(8): 766-82, 2004 Aug.
Article in English | MEDLINE | ID: mdl-15219561

ABSTRACT

A molecular phylogenetic analysis of the genus Phytophthora was performed, 113 isolates from 48 Phytophthora species were included in this analysis. Phylogenetic analyses were performed on regions of mitochondrial (cytochrome c oxidase subunit 1; NADH dehydrogenase subunit 1) and nuclear gene sequences (translation elongation factor 1alpha; beta-tubulin) and comparisons made to test for incongruence between the mitochondrial and nuclear data sets. The genus Phytophthora was confirmed to be monophyletic. In addition, results confirm that the classical taxonomic grouping as described by [Waterhouse (1963)] does not reflect true phylogenetic relations. Phytophthora species were redistributed into 8 clades, providing a more accurate representation of phylogenetic relationships within the genus Phytophthora. The evolution and transition of morphological, pathogenic, and reproductive traits was inferred from the cladogram generated in this study. Mating system was inferred to be a homoplasious trait, with at least eight independent transitions from homothallism to heterothallism observed.


Subject(s)
Cell Nucleus/genetics , DNA, Mitochondrial/classification , DNA/classification , Phylogeny , Phytophthora/classification , Biological Evolution , Electron Transport Complex IV/classification , Electron Transport Complex IV/genetics , Molecular Sequence Data , NADH Dehydrogenase/classification , NADH Dehydrogenase/genetics , Open Reading Frames/genetics , Peptide Elongation Factor 1/classification , Peptide Elongation Factor 1/genetics , Phytophthora/genetics , Sequence Analysis, DNA , Tubulin/classification , Tubulin/genetics
9.
Phytopathology ; 92(5): 464-77, 2002 May.
Article in English | MEDLINE | ID: mdl-18943020

ABSTRACT

ABSTRACT The population structure of Guignardia citricarpa sensu lato (anamorph: Phyllosticta citricarpa), a fungus of which strains pathogenic to citrus are subject to phytosanitary legislation in the European Union and the United States, was investigated. Internal transcribed spacer sequences revealed two phylogenetically distinct groups in G. citricarpa. This distinction was supported by amplified fragment length polymorphism analysis that also supported the exclusion of two isolates that had apparently been misclassified as G. citricarpa. On cherry decoction agar, but not on other media, growth rates of group I isolates were lower than those of group II isolates. Conidial dimensions were similar, but group I isolates formed conidia with barely visible mucoid sheaths, whereas those of group II formed conidia with thick sheaths. Cultures of isolates belonging to group I produced rare infertile perithecia, whereas fertile perithecia were formed by most isolates of group II. Colonies of isolates belonging to group I were less dark than those of group II, with a wider translucent outer zone and a lobate rather than entire margin. On oatmeal agar, exclusively group I isolates formed a yellow pigment. Group I harbored strains from citrus fruits with classical black spot lesions (1 to 10 mm in diameter) usually containing pycnidia. Group II harbored endophytic strains from a wide range of host species, as well as strains from symptomless citrus fruits or fruits with minute spots (<2-mm diameter) without pycnidia. These observations support the historic distinction between slowly growing pathogenic isolates and morphologically similar fast-growing, nonpathogenic isolates of G. citricarpa. The latter proved to belong to G. mangiferae (P. capitalensis), a ubiquitous endophyte of woody plants with numerous probable synonyms including G. endophyllicola, G. psidii, P. anacardiacearum, and P. theacearum. G. mangiferae occurs in the European Union and the United States on many host species including citrus, and does not cause symptoms of citrus black spot, justifying its exclusion from quarantine measures.

11.
Article in English | MEDLINE | ID: mdl-12425020

ABSTRACT

Foot and root rot in cucumber, caused by Pythium aphanidermatum (Edson) Fitzp., is an economically important disease in soilless culture systems. Nevertheless, very few data are available on the populations of this pathogen. Therefore, two detection methods, nested PCR (polymerase chain reaction) and plating on a selective medium after concentration of samples, were optimised and evaluated. With both methods very low concentrations of P. aphanidermatum could be detected; i.e. the detection limits were around 0.05 CFU/ml nutrient solution. In addition, real-time quantitative PCR using a Molecular Beacon probe was designed and tested. The potential and limitations of the different detection methods are discussed. With these different detection techniques, the population dynamics of P. aphanidermatum in a cucumber crop was followed. The impact of different disinfection treatments was studied in a greenhouse experiment with a cucumber crop growing on rockwool slabs in 12 independent closed systems. The nutrient solution was recirculated without disinfection (control), after UV-irradiation (250 mJ/cm2), or after slow sand filtration treatment. Part of the crop was inoculated with an isolate of P. aphanidermatum. The non-inoculated part could only become infected through the recirculated nutrient solution. Disease symptoms (stem rot, wilt, and root rot) and the yield loss were recorded in addition to the population dynamics of the pathogen. Very clear differences in the spread of the pathogen and in disease symptoms were measured between the systems with and without disinfection. UV-irradiation and slow sand filtration were both effective in removing the pathogen and protected the crop from disease symptoms. Correlation indices between the final yield and the different measurements during the experiment were calculated.


Subject(s)
Cucumis sativus/microbiology , Plant Diseases/microbiology , Pythium/growth & development , Colony Count, Microbial , Culture Media , DNA, Fungal/isolation & purification , Filtration , Plant Roots/microbiology , Polymerase Chain Reaction , Population Dynamics , Pythium/genetics , Pythium/radiation effects , Ultraviolet Rays
12.
Phytopathology ; 90(8): 867-74, 2000 Aug.
Article in English | MEDLINE | ID: mdl-18944508

ABSTRACT

ABSTRACT Hybrid isolates of Phytophthora nicotianae x P. cactorum from five different hosts (Cyclamen, Lavandula, Lewisia, Primula, and Spathiphyllum spp.) were identified by their atypical morphology and their well-defined heterozygous isozyme patterns. The hybrid nature of these isolates was tested by restriction fragment length polymorphism analysis of the internal transcribed spacer (ITS) region of rDNA, generating fragments typical for both P. nicotianae and P. cactorum. In hybrid isolates, polymerase chain reactions (PCR) with primers derived from unique parts of the ITS region (ITS-PCR) of both species yielded a combination of unique amplicons typical of both parental species. Eleven hybrid isolates, three isolates of each parental species and two atypical isolates from Rhododendron and Idesia spp. close to P. cactorum, were analyzed for amplified fragment length polymorphisms (AFLP). Consistent differences in AFLP patterns existed among the hybrid isolates, strongly indicating that these hybrids have arisen from independent hybridization events between P. nicotianae and P. cactorum. The two atypical isolates morphologically resembling P. cactorum were identical to the latter species in ITS-restriction fragment length polymorphism and response to the specific PCR primers but were intermediate between P. nicotianae x P. cactorum and P. cactorum in isozyme profiles and AFLP patterns. Since the introduction of hydroponic systems in greenhouses in the Netherlands, outbreaks of Phytophthora diseases are occurring in previously unaffected host species. This may be due to interspecific hybridization events resulting in novel pathogenic behavior.

13.
Phytopathology ; 90(8): 891-900, 2000 Aug.
Article in English | MEDLINE | ID: mdl-18944511

ABSTRACT

ABSTRACT The monophyletic origin of host-specific taxa in the plant-pathogenic Fusarium oxysporum complex was tested by constructing nuclear and mitochondrial gene genealogies and amplified fragment length polymorphism (AFLP)-based phylogenies for 89 strains representing the known genetic and pathogenic diversity in 8 formae speciales associated with wilt diseases and root and bulb rot. We included strains from clonal lineages of F. oxysporum f. spp. asparagi, dianthi, gladioli, lilii, lini, opuntiarum, spinaciae, and tulipae. Putatively nonpathogenic strains from carnation and lily were included and a reference strain from each of the three main clades identified previously in the F. oxysporum complex; sequences from related species were used as outgroups. DNA sequences from the nuclear translation elongation factor 1alpha and the mitochondrial small subunit (mtSSU) ribosomal RNA genes were combined for phylogenetic analysis. Strains in vegetative compatibility groups (VCGs) shared identical sequences and AFLP profiles, supporting the monophyly of the two single-VCG formae speciales, lilii and tulipae. Identical genotypes were also found for the three VCGs in F. oxysporum f. sp. spinaciae. In contrast, multiple evolutionary origins were apparent for F. oxysporum f. spp. asparagi, dianthi, gladioli, lini, and opuntiarum, although different VCGs within each of these formae speciales often clustered close together or shared identical EF-1alpha and mtSSU rDNA haplotypes. Kishino-Hasegawa analyses of constraints forcing the monophyly of these formae speciales supported the exclusive origin of F. oxysporum f. sp. opuntiarum but not the monophyly of F. oxysporum f. spp. asparagi, dianthi, gladioli, and lini. Most of the putatively nonpathogenic strains from carnation and lily, representing unique VCGs, were unrelated to F. oxysporum f. spp. dianthi and lilii, respectively. Putatively nonpathogenic or rot-inducing strains did not form exclusive groups within the molecular phylogeny. Parsimony analyses of AFLP fingerprint data supported the gene genealogy-based phylogram; however, AFLP-based phylogenies were considerably more homoplasious than the gene genealogies. The predictive value of the forma specialis naming system within the F. oxysporum complex is questioned.

14.
Phytopathology ; 88(9): 922-9, 1998 Sep.
Article in English | MEDLINE | ID: mdl-18944870

ABSTRACT

ABSTRACT Three similar isolates of Phytophthora (Phytophthora sp-h) were obtained from diseased Spathiphyllum and Primula plants. Cultural characteristics did not fit any known description of Phytophthora species. The Phytophthora sp-h isolates are papillate, are homothallic, possess 80 to 86% amphigynous antheridia, and have a maximum temperature for growth of 36.5 degrees C. Isozyme analysis of the Phytophthora sp-h isolates revealed a three-banded pattern with malic enzyme and a three-banded pattern with malate dehydrogenase on the second putative locus. The fastest band at both enzyme loci comigrated with the single P. nicotianae band, the slowest band comigrated with the single P. cactorum (and also P. pseudotsugae) band, and one band in between was concluded to represent the heterodimeric isozyme. The random amplified polymorphic DNA patterns of the Phytophthora sp-h isolates almost exclusively consisted of bands that were also present in either P. nicotianae or P. cactorum. Southern hybridization showed that bands specific for P. nicotianae were present as comigrating bands in the Phytophthora sp-h isolates. The same was found for species-specific bands of P. cactorum. It is concluded that the three Phytophthora sp-h isolates represent interspecific hybrids, P. nicotianae being the one parent and P. cactorum the other. Analysis of mito-chondrial DNA with restriction enzymes revealed banding patterns in all the Phytophthora sp-h isolates identical with those of P. nicotianae, confirming that indeed P. nicotianae was one of the parents.

15.
Microbiology (Reading) ; 141 ( Pt 4): 775-84, 1995 Apr.
Article in English | MEDLINE | ID: mdl-7773385

ABSTRACT

Scanning electron micrographs of the nematode-egg-parasitic fungus Paecilomyces lilacinus infecting eggs of the root-knot nematode Meloidogyne spp. suggested the involvement of lytic enzymes. When grown on a liquid mineral salts medium, supplemented with different substrates as the sole N- and C-source, the fungus produced an extracellular protease. Colloidal chitin, vitellin and intact eggs of the root-knot nematode Meloidogyne hapla induced proteolytic activity that was repressed by glucose. The protease was partially purified from the culture filtrate by affinity chromatography. It has a molecular mass of 33.5 kDa, a pH optimum of 10.3, a temperature optimum of 60 degrees C and an isoelectric point above pH 10.2. The enzyme was completely inhibited by PMSF. The amino acid sequence, as derived from the nucleotide sequence of a cDNA clone, had high homology with several subtilisin-like serine proteases. It was shown that the purified enzyme degrades vitellin. The protease quantitatively bound to nematode eggs, and eggs incubated with the purified protease eventually floated. Incubation of the purified protease with nematode eggs significantly influenced their development as demonstrated by time-lapse microscopy. Immature eggs were highly vulnerable to protease treatments, whereas those containing a juvenile were more resistant. In addition, hatched larvae were not visibly affected by the protease. It can be concluded that the serine protease might play a role in penetration of the fungus through the egg-shell of nematodes.


Subject(s)
Paecilomyces/enzymology , Serine Endopeptidases/pharmacology , Tylenchoidea/microbiology , Amino Acid Sequence , Animals , Base Sequence , DNA, Complementary/genetics , DNA, Fungal/genetics , Female , Hydrogen-Ion Concentration , Isoelectric Point , Molecular Sequence Data , Molecular Weight , Ovum/drug effects , Ovum/microbiology , Paecilomyces/growth & development , Paecilomyces/physiology , Pest Control, Biological , Sequence Homology, Amino Acid , Serine Endopeptidases/chemistry , Serine Endopeptidases/genetics , Tylenchoidea/drug effects
16.
Eur J Biochem ; 190(3): 531-7, 1990 Jul 05.
Article in English | MEDLINE | ID: mdl-2115440

ABSTRACT

31P-nuclear-magnetic-resonance spectroscopy has been employed to probe the structure of the detergent-solubilized form of liver microsomal NADPH--cytochrome-P-450 reductase. In addition to the resonances due to the FMN and FAD coenzymes, additional phosphorus resonances are observed and are assigned to the tightly bound adenosine 2'-phosphate (2'-AMP) and to phospholipids. The phospholipid content was found to vary with the preparation; however, the 2'-AMP resonance was observed in all preparations tested. In agreement with published results [Otvos et al. (1986) Biochemistry 25, 7220-7228] for the protease-solubilized enzyme, the addition of Mn(II) to the oxidized enzyme did not result in any observable line-broadening of the FMN and FAD phosphorus resonances. The phospholipid resonances, however, were extensively broadened and the line width of the phosphorus resonance assigned to the bound 2'-AMP was broadened by approximately 70 Hz. The data show that only the phosphorus moieties of the phospholipids and the 2'-AMP, but not the flavin coenzymes are exposed to the bulk solvent. Removal of the FMN moiety from the enzyme substantially alters the 31P-NMR spectrum as compared with the native enzyme. The 2'-AMP is removed from the enzyme during the FMN-depletion procedure and the pyrophosphate resonances of the bound FAD are significantly altered. Reconstitution of the FMN-depleted protein with FMN results in the restoration of the coenzyme spectral properties. Reduction of FMN to its air-stable paramagnetic semiquinone form results in broadening of the FMN and 2'-AMP resonances in the detergent-solubilized enzyme. In agreement with previous results. FMN semiquinone formation had little or no effect on the line width of the FMN phosphorus resonance for the proteolytically solubilized enzyme. 31P-NMR experiments with Azotobacter flavodoxin semiquinone, both in its free form and in a complex with spinach ferredoxin-NADP+ reductase, mimic the differential paramagnetic effects of the flavin semiquinone on the line width of the FMN phosphorus resonance, observed by comparison of the detergent-solubilized and protease-solubilized forms of the reductase. The data demonstrate that assignment of the site of flavin semiquinone formation to a particular flavin coenzyme may not always be possible by 31P-NMR experiments in multi-flavin containing enzymes.


Subject(s)
Azotobacter/enzymology , Ferredoxin-NADP Reductase/metabolism , Flavodoxin/metabolism , Flavoproteins/metabolism , NADH, NADPH Oxidoreductases/metabolism , NADPH-Ferrihemoprotein Reductase/metabolism , Animals , Binding Sites , Flavin Mononucleotide/metabolism , Flavin-Adenine Dinucleotide/metabolism , Magnetic Resonance Spectroscopy/methods , Microsomes, Liver/enzymology , Phosphorus , Protein Binding , Rabbits , Swine
17.
Biochemistry ; 28(21): 8416-25, 1989 Oct 17.
Article in English | MEDLINE | ID: mdl-2513878

ABSTRACT

Fluorescence as well as fluorescence anisotropy decay parameters have been obtained from NADPH-cytochrome P-450 reductase by time-resolved fluorescence spectroscopy. The two flavins in the enzyme, FMN and FAD, are slightly fluorescent and exhibit heterogeneous fluorescence lifetimes, as observed with other flavoproteins. The time-dependent anisotropy is also multiexponential and is wavelength-dependent. The anisotropy decay is biexponential with two correlation times when the enzyme is excited at the red edge of the first absorption band (514 nm). When the enzyme is excited in the light absorption maximum (458 nm), an additional shorter correlation time is found, which contains information about the rate of energy transfer between the two flavins present in the enzyme. FMN-depleted NADPH-cytochrome P-450 reductase shows also only two correlation times, as does the enzyme in the "air-stable" semiquinone state when excited at 458 nm. Wavelength-dependent steady-state anisotropy measurements of native and FMN-depleted protein show that the former exhibits lower values than the latter in the region of the first absorption band, but when the red edge of the absorption band is reached, the anisotropy becomes equal in both preparations. A similar situation is encountered in model compounds, monomeric and dimeric flavins, immobilized in poly(methyl methacrylate). Both in the models and in the flavoprotein this can be attributed to failure of energy transfer at the red edge of the absorption band. From the results we were able to derive both geometric parameters and dynamic properties of both flavins in the NADPH-cytochrome P-450 reductase.(ABSTRACT TRUNCATED AT 250 WORDS)


Subject(s)
NADPH-Ferrihemoprotein Reductase , Chemical Phenomena , Chemistry, Physical , Energy Transfer , Flavin Mononucleotide , Flavin-Adenine Dinucleotide , Fluorescence Polarization , Mathematics , Spectrometry, Fluorescence , Time Factors
18.
Ann Clin Biochem ; 20(Pt 3): 174-81, 1983 May.
Article in English | MEDLINE | ID: mdl-6881902

ABSTRACT

A model is postulated describing the fluctuations in analytical chemical processes in the clinical laboratory. In this model the process variations are described by a non-stationary stochastic process with a significant time-varying mean value. Experiments short-term variance within a run and a long-term variance between runs determined by the time-varying mean value. For four different analytical systems used for determining six serum analytes between-run variance was demonstrated to be significantly greater than within-run variance. Based on the model a digital filtering procedure is presented which in each run estimates the process mean and subsequently corrects serum samples for its deviation. Thus significant variance reductions are obtained. The filtering procedure was tested for the determination in inorganic phosphate with a continuous-flow system in an experimental environment.


Subject(s)
Chemistry, Clinical/standards , Analysis of Variance , Humans , Mathematics , Phosphates/blood
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