Inhibition of Ophiognomonia clavigignenti-juglandacearum by Juglans Species Bark Extracts.

A rapid and reliable technique is needed for identifying butternut trees (Juglans cinerea) with resistance to butternut canker. We investigated the potential of a bark extract bioassay to detect levels of resistance to Ophiognomonia clavigignenti-juglandacearum (Oc-j), the causal agent of butternut canker. Both reagent grade naphthoquinones and crude bark extracts of Juglans species inhibited germination of Oc-j conidia. A disc diffusion bioassay was used to study the level of inhibition by these bark extracts and results indicated extensive variation within and between butternut and other species of Juglans tested. In many months over a 3 year period, bark from butternut trees selected for apparent disease resistance could be distinguished from that of unselected trees. Inhibition of conidia germination roughly correlated to the level of resistance observed in field inoculations of the trees. Quantification of the naphthoquinone compounds juglone and plumbagin in butternut bark was performed using ultra-high performance liquid chromatography mass spectrometry. While the concentrations of these two compounds varied by month and by individual tree, juglone levels correlated well with the bark extract bioassay in some months. These results suggest that juglone concentration may account in part for the observed range of inhibition observed in the bioassay and variation in canker resistance among selections of butternut field inoculated with Oc-j. The bark extract bioassay described in the following report may have potential use for selecting resistant butternut for conservation and restoration purposes.

Seasonal pasture myopathy/atypical myopathy in North America associated with ingestion of hypoglycin A within seeds of the box elder tree.

REASONS FOR PERFORMING STUDY: We hypothesised that seasonal pasture myopathy (SPM), which closely resembles atypical myopathy (AM), was caused by ingestion of a seed-bearing plant abundant in autumn pastures. OBJECTIVES: To identify a common seed-bearing plant among autumn pastures of horses with SPM, and to determine whether the toxic amino acid hypoglycin A was present in the seeds and whether hypoglycin metabolites were present in SPM horse serum or urine. METHODS: Twelve SPM cases, 11 SPM pastures and 23 control farms were visited to identify a plant common to all SPM farms in autumn. A common seed was analysed for amino acid composition (n = 7/7) by GC-MS and its toxic metabolite (n = 4/4) identified in conjugated form in serum [tandem mass spectrometry (MS/MS)] and urine [gas chromatography (GC) MS]. Serum acylcarnitines and urine organic acid profiles (n = 7) were determined for SPM horses. RESULTS: Seeds from box elder trees (Acer negundo) were present on all SPM and 61% of control pastures. Hypoglycin A, known to cause acquired multiple acyl-CoA dehydrogenase deficiency (MADD), was found in box elder seeds. Serum acylcarnitines and urine organic acid profiles in SPM horses were typical for MADD. The hypoglycin A metabolite methylenecyclopropylacetic acid (MCPA), known to be toxic in other species, was found in conjugated form in SPM horse serum and urine. Horses with SPM had longer turn-out, more overgrazed pastures, and less supplemental feeding than control horses. POTENTIAL RELEVANCE: For the first time, SPM has been linked to a toxin in seeds abundant on autumn pastures whose identified metabolite, MCPA, is known to cause acquired MADD, the pathological mechanism behind SPM and AM. Further research is required to determine the lethal dose of hypoglycin A in horses, as well as factors that affect annual seed burden and hypoglycin A content in Acer species in North America and Europe.

Dehydration is catalyzed by glutamate-136 and aspartic acid-135 active site residues in Escherichia coli dTDP-glucose 4,6-dehydratase.

The dTDP-glucose 4,6-dehydratase catalyzed conversion of dTDP-glucose to dTDP-4-keto-6-deoxyglucose occurs in three sequential chemical steps: dehydrogenation, dehydration, and rereduction. The enzyme contains the tightly bound coenzyme NAD(+), which mediates the dehydrogenation and rereduction steps of the reaction mechanism. In this study, we have determined that Asp135 and Glu136 are the acid and base catalysts, respectively, of the dehydration step. Identification of the acid catalyst was performed using an alternative substrate, dTDP-6-fluoro-6-deoxyglucose (dTDP-6FGlc), which undergoes fluoride ion elimination instead of dehydration, and thus does not require protonation of the leaving group. The steady-state rate of conversion of dTDP-6FGlc to dTDP-4-keto-6-deoxyglucose by each Asp135 variant was identical to that of wt, in contrast to turnover using dTDP-glucose where differences in rates of up to 2 orders of magnitude were observed. These results demonstrate Asp135's role in protonating the glucosyl-C6(OH) during dehydration. The base catalyst was identified using a previously uncharacterized, enzyme-catalyzed glucosyl-C5 hydrogen-solvent exchange reaction of product, dTDP-4-keto-6-deoxyglucose. Base catalysis of this exchange reaction is analogous to that occurring at C5 during the dehydration step of net catalysis. Thus, the decrease in the rate of catalysis ( approximately 2 orders of magnitude) of the exchange reaction observed with Glu136 variants demonstrates this residue's importance in base catalysis of dehydration.

Probing catalysis by Escherichia coli dTDP-glucose-4,6-dehydratase: identification and preliminary characterization of functional amino acid residues at the active site.

A model of the Escherichia coli dTDP-glucose-4,6-dehydratase (4,6-dehydratase) active site has been generated by combining amino acid sequence alignment information with the 3-dimensional structure of UDP-galactose-4-epimerase. The active site configuration is consistent with the partially refined 3-dimensional structure of 4,6-dehydratase, which lacks substrate-nucleotide but contains NAD(+) (PDB file ). From the model, two groups of active site residues were identified. The first group consists of Asp135(DEH), Glu136(DEH), Glu198(DEH), Lys199(DEH), and Tyr301(DEH). These residues are near the substrate-pyranose binding pocket in the model, they are completely conserved in 4,6-dehydratase, and they differ from the corresponding equally well-conserved residues in 4-epimerase. The second group of residues is Cys187(DEH), Asn190(DEH), and His232(DEH), which form a motif on the re face of the cofactor nicotinamide binding pocket that resembles the catalytic triad of cysteine-proteases. The importance of both groups of residues was tested by mutagenesis and steady-state kinetic analysis. In all but one case, a decrease in catalytic efficiency of approximately 2 orders of magnitude below wild-type activity was observed. Mutagenesis of each of these residues, with the exception of Cys187(DEH), which showed near-wild-type activity, clearly has important negative consequences for catalysis. The allocation of specific functions to these residues and the absolute magnitude of these effects are obscured by the complex chemistry in this multistep mechanism. Tools will be needed to characterize each chemical step individually in order to assign loss of catalytic efficiency to specific residue functions. To this end, the effects of each of these variants on the initial dehydrogenation step were evaluated using a the substrate analogue dTDP-xylose. Additional steady-state techniques were employed in an attempt to further limit the assignment of rate limitation. The results are discussed within the context of the 4,6-dehydratase active site model and chemical mechanism.

Characterization of enzymatic processes by rapid mix-quench mass spectrometry: the case of dTDP-glucose 4,6-dehydratase.

The single-turnover kinetic mechanism for the reaction catalyzed by dTDP-glucose 4,6-dehydratase (4,6-dehydratase) has been determined by rapid mix-chemical quench mass spectrometry. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was employed to analyze quenched samples. The results were compatible with the postulated reaction mechanism, in which NAD(+) initially oxidizes glucosyl C4 of dTDP-glucose to NADH and dTDP-4-ketoglucose. Next, water is eliminated between C5 and C6 of dTDP-4-ketoglucose to form dTDP-4-ketoglucose-5,6-ene. Hydride transfer from NADH to C6 of dTDP-4-ketoglucose-5,6-ene regenerates NAD(+) and produces the product dTDP-4-keto-6-deoxyglucose. The single-turnover reaction was quenched at various times on the millisecond scale with a mixture of 6 M guanidine hydrochloride and sodium borohydride, which stopped the reaction and reductively stabilized the intermediates and product. Quantitative MALDI-TOF MS analysis of the quenched samples allowed the simultaneous observation of the disappearance of substrate, transient appearance and disappearance of dTDP-hexopyranose-5,6-ene (the reductively stabilized dTDP-4-ketoglucose-5,6-ene), and the appearance of product. Kinetic modeling of the process allowed rate constants for most of the steps of the reaction of dTDP-glucose-d(7) to be evaluated. The transient formation and reaction of dTDP-4-ketoglucose could not be observed, because this intermediate did not accumulate to detectable concentrations.

Novel genes expressed in the chick otocyst during development: identification using differential display of RNA.

Differential display of mRNA is a technique that enables the researcher to compare genes expressed in two or more different tissues or in the same tissue or cell under different conditions. The method is based on polymerase chain reaction amplification and comparison of specific subsets of mRNA. We have used this method to clone partial complementary DNAs (cDNAs; amplicons) for genes expressed in the otocyst in order to identify genes that may be involved in development of the inner ear. A full length cDNA was isolated from an embryonic quail head library with an amplicon (KH121) obtained from the otocyst. This avian cDNA encoded a novel, 172-amino acid acidic protein and detected a major transcript of ca 0.8 kb in RNA from chick embryos and several neonatal chick tissues. The full length avian cDNA had high sequence identity to several human cDNAs (expressed sequence tags) from human fetal tissues, including cochlea, brain, liver/spleen and lung, and from placenta. The human homologue of the avian gene encoded a protein that was 183 amino acids long and had 75.6% amino acid sequence identity to the avian protein. These results identified both the avian and human homologues of an evolutionarily conserved gene encoding a small acidic protein of unknown function; however, expression of this gene was not restricted to otocysts.

Structural analysis of UDP-sugar binding to UDP-galactose 4-epimerase from Escherichia coli.

UDP-galactose 4-epimerase from Escherichia coli catalyzes the interconversion of UDP-galactose and UDP-glucose through the transient reduction of the tightly bound cofactor NAD+. The enzyme is unique among the NAD+-dependent enzymes in that it promotes stereospecific reduction of the cofactor but nonstereospecific hydride return during normal catalysis. In addition to hydride transfer, the reaction mechanism of epimerase involves two key features: the abstraction of a proton from the 4'-hydroxyl group of glucose or galactose by an active site base and the rotation of a 4-ketopyranose intermediate in the active site pocket. To address the second issue of movement within the active site, the X-ray structures of reduced epimerase complexed with UDP-mannose, UDP-4-deoxy-4-fluoro-alpha-D-galactose, or UDP-4-deoxy-4-fluoro-alpha-D-glucose have been determined and refined to 1.65, 1.8, and 1.65 A resolution, respectively. A comparison of these models to that of the previously determined epimerase/NADH/UDP-glucose abortive complex reveals that the active site accommodates the various sugars by simple rearrangements of water molecules rather than by large changes in side chain conformations. In fact, the polypeptide chains for all of the epimerase/NADH/UDP-sugar complexes studied thus far are remarkably similar and can be superimposed with root-mean-square deviations of not greater than 0.24 A. The only significant differences between the various enzyme/UDP-sugar models occur in two of the dihedral angles defining the conformation of the UDP-sugar ligands.

Identification of genes expressed after noise exposure in the chick basilar papilla.

We used differential display of mRNA, a method based on reverse transcriptase-PCR, to identify genes whose expression increases in response to acoustic trauma in the chick basilar papilla. Identifying these genes would provide insight into processes involved in repair of the damaged epithelium or in hair cell regeneration. We compared mRNA from the basilar papilla of normal chicks, from chicks exposed to an octave band noise (center frequency: 1.5 kHz) presented at 118 dB for 6 h, and from chicks exposed to noise and allowed to recover for 2 days. Thus far, we have identified 70 bands that appear to be differentially displayed on DNA sequencing gels; approximately 40 of these bands have been subcloned and sequenced. DNA sequences were compared with sequences in the GenBank database to identify genes with significant (70-85%) sequence identity to known genes. Chick cDNAs identified included: the parathyroid hormone-related protein, an immediate early gene; the delta-subunit of the neuronal-specific Ca2+/calmodulin-regulated protein kinase II; and the GTP-binding protein CDC42, a member of the ras superfamily of G proteins. A fourth cDNA had 84% sequence identity to an uncharacterized human cDNA (expressed sequence tag), indicating that this is a novel gene. Slot-blot hybridization analysis of these cDNAs probed with labeled DNA generated from mRNA from each experimental group indicated higher levels of mRNA for each of these four genes after noise exposure. These results indicate the potential involvement of both Ca2+/calmodulin-mediated signaling and GTPase cascades in the response to noise damage and during hair cell regeneration in the chick basilar papilla.

Sequence of the cDNA for the heart/muscle isoform of mouse cytochrome c oxidase subunit VIII.

We have isolated and sequenced cDNAs for the heart/muscle (H) isoform of mouse cytochrome c oxidase subunit VIII (COX VIII-H). The deduced protein sequence enables us to compare the heart/muscle COX VIII isoforms from several species and to determine that the most highly conserved region of this subunit is the C-terminal domain.