An X-ray structural study of human ceruloplasmin in relation to ferroxidase activity

The role of ceruloplasmin as a ferroxidase in the blood, mediating the release of iron from cells and its subsequent incorporation into serum transferrin, has long been the subject of speculation and debate. However, a recent X-ray crystal structure determination of human ceruloplasmin at a resolution of around 3.0?Å, in conjunction with studies associating mutations in the ceruloplasmin gene with systemic haemosiderosis in humans, has added considerable weight to the argument in favour of a ferroxidase role for this enzyme. Further X-ray studies have now been undertaken involving the binding of the cations Co(II), Fe(II), Fe(III), and Cu(II) to ceruloplasmin. These results give insights into a mechanism for ferroxidase activity in ceruloplasmin. The residues and sites involved in ferroxidation are similar to those proposed for the heavy chains of human ferritin. The nature of the ferroxidase activity of human ceruloplasmin is described in terms of its three-dimensional molecular structure.     

On the lability and functional significance of the type 1 copper pool in ceruloplasmin

 The possibility that ceruloplasmin (CP) functions as a copper transferase has fueled a continuing interest in studies of the copper release process. The principal goal of the current investigation has been to identify the most labile copper centers in sheep protein. In fact, subjecting the enzyme to a slow flux of cyanide at pH 5.2 under nitrogen in the presence of ascorbate and a phenanthroline ligand produces partially demetalated forms of the protein. By standard chromatographic techniques it is possible to isolate protein with a Cu/CP ratio of ∼4 or ∼5 as opposed to the native protein which has Cu/CP=5.8. In contrast to other blue oxidases, analysis suggests that CP preferentially loses its type 1 coppers under these conditions. Thus, the spectroscopic signals from the type 1 centers exhibit a loss of intensity while the EPR signal of the type 2 copper becomes stronger. Furthermore, the Cu/CP≈4 and Cu/CP≈5 components retain about 50% of the activity of the native protein, consistent with an intact type 2/type 3 cluster. All three type 1 copper sites appear to suffer copper loss. Reconstitution with a copper(I) reagent restores the spectroscopic properties of the native protein and 90% of the original activity. The results suggest a possible functional significance for the presence of three type 1 coppers in CP. By employing a pool of redox-active but relatively labile type 1 copper centers, the enzyme can serve as a copper donor, if necessary, without completely sacrificing its oxidase activity. Received: 15 February 1999 / Accepted: 22 April 1999     

Roles of multiple surface sites,long substrate binding clefts,and carbohydrate binding modules in the action of amylolytic enzymes on polysaccharide substrates

Germinating barley seeds contain multiple forms of α-amylase, which are subject to both differential gene expression and differential degradation as part of the repertoire of starch-degrading enzymes. The α-amylases are endo-acting and possess a long substrate binding cleft with a characteristic subsite binding energy profile around the catalytic site. Furthermore, several amylolytic enzymes that facilitate attack on the natural substrate, i.e. the endosperm starch granules, have secondary sugar binding sites either situated on the surface of the protein domain or structural unit that contains the catalytic site or belonging to a separate starch binding domain. The role of surface sites in the function of barley α-amylase 1 has been investigated by using mutational analysis in conjunction with carbohydrate binding analyses and crystallography. The ability to bind starch depends on the surface sites and varies for starch granules of different genotypes and botanical origin. The surface sites, moreover, are candidates for being involved in degradation of polysaccharides by a multiple attack mechanism. Future studies of the molecular nature of the multivalent enzyme-substrate interactions will address surface sites in both barley α-amylase 1 and in the related isozyme 2.     

Trace element levels in mollusks from clean and polluted coastal marine sites in the Mediterranean, Red and North Seas

The trace element contamination levels in mollusks were evaluated for different marine coastal sites in the Mediterranean (Israeli coast), Red (Israeli coast) and North (German coast) Seas. Three bivalve species (Mactra corallina, Donax sp, and Mytilus edulis) and two gastropod species (Patella sp.and Cellana rota) were sampled at polluted and relatively clean sites, and their soft tissue analyzed for Hg, Cd, Zn, Cu, Mn and Fe concentrations. Representative samples were screened for organic contaminants [(DDE), polychlorinated biphenyls PCBs and polycyclic aromatic hydrocarbons (PAHs)] which exhibited very low concentrations at all sites. In the Red Sea, the gastropod C. rota showed low levels of Hg (below detection limit) and similar Cd concentrations at all the examined sites, while other trace elements (Cu, Zn, Mn, Fe) were slightly enriched at the northern beach stations. Along the Mediterranean coast of Israel, Hg and Zn were enriched in two bivalves (M. corallina and Donax sp.) from Haifa Bay, both species undergoing a long-term decrease in Hg based on previous studies. Significant Cd and Zn enrichment was detected in Patella sp. from the Kishon River estuary at the southern part of Haifa Bay. In general, Patella sp. and Donax sp. specimens from Haifa Bay exhibited higher levels of Cd compared to other sites along the Israeli Mediterranean coast, attributed to the enrichment of Cd in suspended particulate matter. Along the German coast (North Sea) M. edulis exhibited higher concentrations of Hg and Cd at the Elbe and Eider estuaries, but with levels below those found in polluted sites elsewhere. Received: 25 February 1999 / Received in revised form: 22 April 1999 / Accepted: 30 April 1999     

The mean and variance of the number of segregating sites since the last hitchhiking event

 Tight linkage may cause a reduction of nucleotide diversity in a chromosomal region if an advantageous mutation appears in that region which is driven to fixation by directional selection. This process is usually called genetic hitchhiking. If selection is strong, the entire process takes place during a time period of length 2s ln (2N) that is very short relative to 2N generations [s is the selection coefficient of the advantageous mutation and N the effective diploid population size]. On the time scale of 2N generations, which is characteristic for neutral evolution, we may therefore call this process a hitchhiking event. Using coalescent methods, we analyzed a model in which a hitchhiking event occurred in a chromosomal region of zero-recombination in the past at time x. Such a hitchhiking “catastrophe” wipes out completely genetic variation that existed in a population before that time. Standing variation observed at present must therefore be due to mutations that have arisen since time point x. Assuming that all newly arising mutations are neutral, we derived expressions for the expectation, variance and also for the higher moments of the number of nucleotide sites segregating in a sample of n genes as a function of x. The result for the first moment is then used to estimate the time back to the last hitchhiking event based on DNA polymorphism data from Drosophila. Assuming that directional selection is the sole determinant of the level of genetic variation in the gene regions surveyed, we obtained estimates of x that were typically in the order of 0.1N generations. Received 14 May 1996; received in revised form 26 August 1996     

Protein- and pH-dependent binding of nascent pectin and glucuronoarabinoxylan to xyloglucan in pea

 Nascent pectin and glucuronoarabinoxylan, synthesised in vitro by membrane-bound enzymes from etiolated pea (Pisum sativum L.) epicotyls, were found to bind to pea xyloglucan in a pH-dependent manner. The binding was maximum at low pH (3–4), and decreased to almost zero at pH 6. The binding was probably non-covalent and reached saturation within 5 min. Removal of the fucose residues of xyloglucan decreased the degree of binding. Removal by protease of the proteins attached to nascent pectin and glucuronoarabinoxylan greatly reduced the maximum binding and abolished the pH-dependence. The observed binding may be of considerable significance in the process of cell-wall assembly and in the control of cell extension. Received: 4 November 1999 / 22 December 1999     

Infrared evidence of azide binding to iron, copper, and non-metal sites in heart cytochrome c oxidase.

Interactions of azide ion with bovine heart cytochrome c oxidase (CcO) at five redox levels (IV) to (0), obtained by zero to four electron reduction of fully oxidized enzyme CcO(IV), were monitored by infrared and visible/Soret spectra. Partially reduced CcO gave three azide asymmetric stretch band at 2040, 2016, and 2004 cm-1 for CcO(III)N3 and two at 2040 and 2016 cm-1 for CcO(II)N3 and CcO(I)N3. Resting CcO(IV) reacts with N3- to give one band at 2041 cm-1 assigned to CuB2+N3 and another at 2051 cm-1 to N3- that is associated with protein but is not bound to a metal ion. At high azide concentrations the weak association of many azide molecules with non-metal protein sites was observed at all redox levels. These findings provide direct evidence for 1) N3- binding to CuB as well as Fea3 in partially reduced enzyme, but no binding to Fea3 in fully oxidized enzyme and no binding to either metal in fully reduced enzyme; 2) a long range effect of the oxidation state of Fea or CuA on ligand binding at heme a3, but not at CuB; and 3) an insensitivity of either Fea3 or CuB ligand site to changes in ligand or oxidation state at the other site. The observed independence of the Fea3 and CuB sites provides further support for Fea3(3)+ OOH, rather than Fea3(3)+ OOCuB2+, as an intermediate in the reduction of O2 to water by the oxidase.     

Polymorphism, distribution, and segregation of AFLP markers in a doubled haploid rice population

We exploited the newly developed amplified fragment length polymorphism (AFLP) technique to study the polymorphism, distribution and inheritance of AFLP markers with a doubled haploid rice population derived from ‘IR64’/‘Azucena’. Using only 20 pairs of primer combinations, we detected 945 AFLP bands of which 208 were polymorphic. All 208 AFLP markers were mapped and distributed over all 12 chromosomes. When these were compared with RFLP markers already mapped in the population, we found the AFLP markers to be highly polymorphic in rice and to follow Mendelian segregation. As linkage map of rice can be generated rapidly with AFLP markers they will be very useful for marker-assisted backcrossing. Received: 11 April 1996 / Accepted: 14 June 1996     

Soybean Kunitz, C-II and PI-IV inhibitor genes confer different levels of insect resistance to tobacco and potato transgenic plants

In modern, highly intensive agriculture, the control of insect pests is basically achieved with the application of chemical pesticides. Heavy reliance on this sole strategy is associated with several drawbacks, and the development of alternative or complementary methods to chemical control is desirable. In this work, three soybean genes (KTi ₃ , C-II and PI-IV)coding for serine proteinase inhibitors were isolated by PCR and transferred to Agrobacterium tumefaciens EHA 105, which in turn was used for transforming tobacco leaf and potato tuber discs. Biochemical assays confirmed that transgenic plants synthesized serine proteinase inhibitors; rates of expression varied among plants. The level of insect resistance (tested with Spodoptera littoralis Boisduval) was particularly high in tobacco, where many plants caused the death of all larvae. In potatoes, larval mortality was much less frequently achieved, but the results were still encouraging in that larval weight gain was reduced by 50% in the presence of adequate amounts of inhibitor. When 8-day-old larvae were fed different KTi ₃ -expressing tobacco plants, a highly significant (P<0.01) correlation was observed between inhibitor content and larval live weight. Larval weight gain was found to be dependent on midgut proteolytic activity. On the basis of the evidence collected, it is suggested that further work is required to identify more specific inhibitors for the main proteinases of the target insect. Received: 30 March 1998 / Accepted: 9 December 1999     

Influence of organic amendments on arbuscular mycorrhizal fungi in relation to rice sheath blight disease

 The effect of various organic soil amendments on arbuscular myorrhizal (AM) fungal activity on rice plants was tested under greenhouse and field conditions with reference to sheath blight (ShB) disease caused by Rhizoctonia solani. AM spore density, per cent infection, and intensity of infection were increased by organic amendments, whilst ShB disease was decreased. Certain amendments, especially green leaf manure, stimulated arbuscule development in rice plants. Mycorrhiza formation and sporulation were higher with healthy rice plants than with rice plants infected with R. solani. Our results indicate the possibility of using selective organic amendments to enhance development of native AM fungi and thus reduce disease incidence. Accepted: 9 November 1995     

Properties of the Trp290His variant of Fusarium NRRL 2903 galactose oxidase: interactions of the GOasesemi state with different buffers, its redox activity and ability to bind azide

The indole ring of Trp-290 in galactose oxidase has an important role in restricting entry to the substrate-binding (Cu) site of galactose oxidase via a short ～8?Å access pocket/channel. It also overlays and helps stabilise the radical-forming Cu-coordinated Tyr-272, reduction potential 400?mV. In this paper the effect of replacing Trp-290 by the less bulky His residue is explored at 25??°C, I=0.100?M (NaCl), and different effects are quantified. Interactions with buffers, not observed in the case of wild-type (WT) GOase, have been investigated by UV-Vis spectrophotometry on the non-radical GOase_semi (Cu^II) form of the Trp290His variant. Equilibrium constants K _eq/M^–1 from absorbance changes at 635?nm are for 1?:?1 interactions with the OH-containing buffers H₂PO₄ ^– (231), Hepes (43) and Tris (202), concentrations 0–60?mM. No similar interactions are observed with Mes, Lutidine and Ches, when significantly different UV-Vis spectra with no peak at ～635?nm are obtained. At pH 7.5 the reduction potential for the Trp290His GOase_ox/GOase_semi couple is 730?mV, which compares with 400?mV for the WT GOase couple. Consistent with the 730?mV value the GOase_semi form is not oxidised with [Fe(CN)₆]^3– (410?mV) or [W(CN)₈]^3– (530?mV), and much stronger oxidants such as [Mo(CN)₈]^3– (800?mV) and [IrCl₆]^2– (890?mV) are required. The GOase_ox product is unstable and decays within 20?min with re-formation of GOase_semi. From changes in UV-Vis spectra with pH, Trp290His GOase_semi gives a pK _a of 6.9, and rate constants for the oxidation of GOase_semi with [Mo(CN)₈]^3– are dependent on this same pK _a. The latter compares with 7.9 for WT GOase_semi, and is assigned here also as protonation of Tyr-495. The 1?:?1 binding of azide at the substrate-binding (H₂O) site of Trp290His GOase_semi was studied and gives a formation constant 330?M^–1 at pH 7.5, which is an order of magnitude less than the corresponding value for WT GOase_semi. The trends observed indicate less affinity of Trp290His GOase_semi for the ionic reactants H⁺ and N₃ ^–.     

A phospholipase inhibitor, manoalide, and a G-protein activator, Mas-7, both affect the turnover of phototransductive membranes by crab retinas in darkness With a model for the regulation of rhabdomeral membrane turnover

(1) In vitro retinas of a crab, Leptograpsus, were treated with a phospholipase inhibitor, manoalide, or a G-protein activator, Mas-7. Both drugs address early stages of the phototransduction cascade. (2) Manoalide inhibited the light-dependent reduction of rhabdoms during the `day' phase of the light cycle, but did not induce rhabdom overgrowth. Following a period of darkness manoalide failed to affect the diminution of illuminated rhabdoms. (3) The diminution of rhabdoms that follows photoreceptor depolarisation induced by 100 mmol · l<sup>−1</sup> K<sup>+</sup> in darkness was not affected by 2␣μmol · l<sup>−1</sup> manoalide. (4) When retinas in the `night' phase were treated with Mas-7 in darkness, rhabdom diameters were augmented, concurrently with endocytosis of photoreceptor plasma membranes. (5) The results of combining manoalide and Mas-7 with actinomycin D, U-57908 or okadaic acid, drugs used in previous studies to manipulate steps notionally lower in the transduction cascade, lead to a hypothetical model for the regulation of phototransductive membrane turnover by arthropods. Accepted: 3 October 1996     

A comparison of AM fungi inoculants using Capsicum and Polianthes in marginal soil amended with organic matter

 Different types of nursery inocula formulations, namely mixed indigenous cultures and Glomus intraradices Schenck and Smith, were compared with commercially available inoculants of AM fungi in a pot experiment using two horticultural crops, Capsicum and Polianthes. Soil-based inocula and soil beads produced the highest response in both crops. Glomus intraradices resulted in the highest yield in both Polianthes (45% increase in spike length) and Capsicum (112% increase in fruit yield). Among the commercial inocula tested, only Mycorise enhanced spike length (33%) and fruit yield (11%) in the two hosts. Overall AM colonization was higher in Polianthes than in Capsicum. Sheared root inocula of G. intraradices resulted in high colonization (upto 68%) but the yield enhancement was lower than with soil-based formulations. The mixed indigenous culture produced the highest number of spores and propagules and commercial inocula the lowest. Accepted: 2 February 1998     

Kinetic studies on the reactions of Fusarium galactose oxidase with five different substrates in the presence of dioxygen

 Reactions (25  °C) of galactose oxidase, GOase_ox from Fusarium NRRL 2903 with five different primary-alcohol-containing substrates RCH₂OH:- D-galactose (I) and 2-deoxy-d-galactose (II) (monosaccharides); methyl-β-d-galactopyranoside (III) (glycoside);d-raffinose (IV) (trisaccharide); and dihydroxyacetone (V) have been studied in the presence of O₂. The GOase_ox state has a tyrosyl radical coordinated at a square-pyramidal Cu^II active site, and is a two-equivalent oxidant. Reactant concentrations were [GOase_ox] (0.8–10 μM), RCH₂OH (1.0–6.0 mM), and O₂ (0.14–0.29 mM), with I=0.100 M (NaCl). The reactions, monitored at 450 nm by stopped-flow spectrophotometry, terminated with depletion of the O₂. Each trace was fitted to the competing reactions GOase_ox+RCH₂ OH → GOase_redH₂+RCHO (k ₁), and GOase_redH₂+O₂→ GOase_ox+H₂O₂ (k ₂), with GOase_redH₂ written as the doubly protonated two-electron-reduced Cu^I product. It was necessary to avoid auto-redox interconversion of GOase_ox and GOase_semi . Information obtained at pH 7.5 indicates a 5 : 95 (ox : semi) "native" mix equilibration complete in ∼3 h. At pH >7.5, rate constants 10^–4 k ₁ / M^–1 s^–1 for the reactions of GOase_ox with (I) (1.19), (II) (1.07), (III) (1.29), (IV) (1.81), (V) (2.94) were determined. On decreasing the pH to 5.5, k ₁ values decreased by factors of up to a half, and acid dissociation pK _as in the range 6.6–6.9 were obtained. UV-Vis spectrophotometric studies on GOase_ox gave an independently determined pK _a of 6.7. No corresponding reactions of the Tyr495Phe variant were observed, and there are no similar UV-Vis absorbance changes for this variant. The pK _a is therefore assigned to protonation of Tyr-495 which is a ligand to the Cu. The rate constant k ₂ (1.01×10⁷ M^–1 s^–1) is independent of pH in the range 5.5–9.0 investigated, suggesting that H⁺ (or H-atoms) for the O₂ → H₂O₂ change are provided by the active site of GOase_red . The Cu^I of GOase_red is less extensively complexed, and a coordination number of three is likely. Received: 4 February 1997 / Accepted: 16 May 1997     

Determining the binding mode and binding affinity constant of tyrosine kinase inhibitor PD153035 to DNA using optical tweezers

Accurately predicting binding affinity constant (K_A) is highly required to determine the binding energetics of the driving forces in drug–DNA interactions. Recently, PD153035, brominated anilinoquinazoline, has been reported to be not only a highly selective inhibitor of epidermal growth factor receptor but also a DNA intercalator. Here, we use a dual-trap optical tweezers to determining K_A for PD153035, where K_A is determined from the changes in B-form contour length (L) of PD153035–DNA complex. Here, L is fitted using a modified wormlike chain model. We found that a noticeable increment in L in 1 mM sodium cacodylate was exhibited. Furthermore, our results showed that K_A = 1.18(±0.09) × 10⁴ (1/M) at 23 ± 0.5 °C and the minimum distance between adjacent bound PD153035 ≈ 11 bp. We anticipate that by using this approach we can determine the complete thermodynamic profiles due to the presence of DNA intercalators.     

Comparative mutant analysis of Arabidopsis ABCC-type ABC transporters: AtMRP2 contributes to detoxification, vacuolar organic anion transport and chlorophyll degradation

The enormous metabolic plasticity of plants allows detoxificationof many harmful compounds that are generated during biosyntheticprocesses or are present as biotic or abiotic toxins in theirenvironment. Derivatives of toxic compounds such as glutathioneconjugates are moved into the central vacuole via ATP-bindingcassette (ABC)-type transporters of the multidrug resistance-associatedprotein (MRP) subfamily. The Arabidopsis genome contains 15AtMRP isogenes, four of which (AtMRP1, 2, 11 and 12) clustertogether in one of two major phylogenetic clades. We isolatedT-DNA knockout alleles in all four highly homologous AtMRP genesof this clade and subjected them to physiological analysis toassess the function of each AtMRP of this group. None of thesingle atmrp mutants displayed visible phenotypes under controlconditions. In spite of the fact that AtMRP1 and AtMRP2 hadbeen described as efficient ATP-dependent organic anion transportersin heterologous expression experiments, the contribution ofthree of the AtMRP genes (1, 11 and 12) to detoxification ismarginal. Only knockouts in AtMRP2 exhibited a reduced sensitivitytowards 1-chloro-2,4-dinitrobenzene, but not towards other herbicides.AtMRP2 but not AtMRP1, 11 and 12 is involved in chlorophylldegradation since ethylene-treated rosettes of atmrp2 showedreduced senescence, and AtMRP2 expression is induced duringsenescence. This suggests that AtMRP2 is involved in vacuolartransport of chlorophyll catabolites. Vacuolar uptake studiesdemonstrated that transport of typical MRP substrates was reducedin atmrp2. We conclude that within clade I, only AtMRP2 contributessignificantly to overall organic anion pump activity in vivo.     

An assay system to study migratory behavior of cranial neural crest cells in Xenopus

An increasing number of genes are known to show expression in the cranial neural crest area. So far it is very difficult to analyze their effect on neural crest cell migration because of the lack of transplantation techniques. This paper presents a simple method to study the migratory behavior of cranial neural crest cells by homo- and heterotopic transplantations: Green fluorescent protein (GFP) RNA was injected into one blastomere of Xenopus laevis embryos at the 2-cell stage. The cranial neural crest area of stage 14 embryos was transplanted into the head or trunk region of an uninjected host embryo, and the migration was monitored by GFP fluorescence. The transplants were further examined by double immunostaining and confocal microscopy to trace migratory routes inside the embryo, and to exclude contaminations of grafts with foreign tissues. Our results demonstrate that we developed a highly efficient and reproducible technique to study the migratory ability of cranial neural crest cells. It offers the possibility to analyze genes involved in neural crest cell migration by coinjecting their RNA with that of GFP. Received: 28 September 1999 / Accepted: 17 November 1999     

Mapping of two genes for resistance to clubroot (Plasmodiophora brassicae) in a population of doubled haploid lines of Brassica oleracea by means of RFLP and AFLP markers

A genetic map covering 615 cM in 12 linkage groups was assembled based on 92 RFLP and AFLP markers segregating in a population of 107 doubled haploid lines (DH lines) of Brassica oleracea. The DH-line population was obtained through microspore culture from the of two homozygous parents: DH-line Bi derived from the cabbage landrace Bindsachsener, and DH-line Gr from broccoli cv ‘Greenia’. Sixty-five percent of the loci, and in some cases complete linkage groups, displayed distorted segregation ratios, a frequency much higher than that observed in populations of the same species. DH-line Bi was resistant to clubroot, which is caused by a Dutch field isolate of Plasmodiophora brassicae. Resistance in the DH-line population was determined in two ways: by assigning symptom grades to each plant, and by measuring the fresh weights of the healthy and affected parts of the root system of each plant. Using a multiple QTL mapping approach to analyze the fresh weight data, we found two loci for clubroot resistance; these were designated pb-3 and pb-4. The additive effects of these loci were responsible for 68% of the difference between the parents and for 60% of the genetic variance among DH-line means. Also, indications for the presence of two additional, minor QTLs were found. Analysis of symptom grades revealed the two QTLs pb-3 and pb-4, as well as one of the two minor QTLs indicated by analysis of the fresh weight data. Received: 29 April 1996 / Accepted: 10 May 1996