The core element of the EcoRII methylase as defined by protease digestion and deletion analysis.

Binding of the EcoRII DNA methyltransferase to azacytosine-containing DNA protects the enzyme from digestion by proteases. The limit digest yields a product having a Mr on SDS-PAGE 20% less than the intact protein. The N terminus of the tryptic digestion product was sequenced and found to be missing the N terminal 82 amino acids. Under the conditions used unbound enzyme was digested to small peptides. Protection of the enzyme from protease digestion implies that the enzyme undergoes major conformational changes when bound to DNA. The trypsin sensitive region of the EcoRII methyltransferase occurs prior to the first constant region shared with other procaryotic DNA(cytosine-5)methyltransferases. To determine if this region played a role in substrate binding or specificity, N-terminal deletion mutants were studied. Deletion of 97 amino acids resulted in a decrease of enzyme activity. Further deletions caused a complete loss of activity. Enzyme deleted through amino acid 85 was purified and found to have the same specificity as wild type however there was an increase in Km for both S-adenosylmethionine (AdoMet) and DNA of 27 and 18 fold respectively. The N-terminus of the EcoRII methylase, although a variable region present in many procaryotic DNA(cytosine-5)methylases, plays no role in determining enzyme specificity, although it does contribute to the interaction with both AdoMet and DNA.     

Utility of internal markers to improve the accuracy of cystic fibrosis genotype analysis.

DNA diagnostic tests often utilize restriction endonuclease digestion of PCR-amplified portions of genes under analysis. When partial digestion occurs, the resulting patterns may lead to error in diagnosis. To overcome such potential errors in cystic fibrosis testing, we have developed internal markers that can increase the precision and reliability of genotype assignments.     

Diagnosis of mycobacterial infections by PCR and restriction enzyme digestion

A method for the diagnosis of mycobacterial infections by PCR amplification followed by selective restriction enzyme digestion of the PCR product was developed. The amplified DNA sequence used in this study occurs within the gene encoding for the mycobacterial 65 kDa heat shock protein (Hance et al. 1989), which is found in all mycobacteria. However, there are minute differences in the amplified sequence from the Mycobacterium tuberculosis complex compared with the corresponding sequence from the Mycobacterium avium complex. These differences made it possible to rapidly identify to which mycobacterial complex a particular sample belonged by restriction enzyme digestion of the PCR product. A total of 66 samples were tested and all of them were correctly identified. This and similar methods should provide a sensitive, specific and rapid (within 12 h) way of diagnosing mycobacterial infections to the species level.     

Solubilization of cheese whey protein by trypsin and a process to recover the active enzyme from the digest

Porcine trypsin (EC 3.4.4.4) converted, within approximately 2 hr at 50°C, its 1000-fold weight of water-insoluble, heat-denaturated cheese whey protein into a water-soluble product. In the course of this digestion, the enzyme increased the α-amino nitrogen of the protein by a factor of >20, from 0.40 to 9.40%. After digesting the water-insoluble whey protein, fully active trypsin could be recovered from the soluble digest with the aid of a cellulose-based affinity adsorbent. The enzyme which was eluted from a column of p-aminobenzamidine, bound to succinylated aminododecylcellulose, was fully active and showed essentially unchanged kinetic properties with a synthetic substrate, L -benzoyl-arginine p-nitroanilide. It was possible to perform, with the same amount of trypsin, three subsequent and equally effective solubilizations of whey protein, followed by a fourth digestion which still yielded a soluble product, but was considerably slower and incomplete. During each digestion, an estimated 30% of the trypsin was lost. The was not due to a decreased efficiency of the affinity adsorbent, as its trypsin-binding capacity was essentially unaffected after over 10 cycles of use.     

Morphological aspects of blood digestion in a parasitic mite Bakericheyla chanayi

All life stages of B. chanayi (Acariformes: Cheyletidae) are characterized by occasional bloodsucking and a long period of digestion. No newly engorged mites were found during the period of their host birds' migration. The fine structure of the digestive tract of a blood-feeding acariform mite is described for the first time. The anterior midgut (AMG) is a place of blood digestion, while the posterior midgut (PMG) is involved in nitrogen metabolism forming guanine crystals as the main end-product. The AMG epithelium consists of digestive cells that probably arise from mitotically active basal cells with high synthesizing activity.As observed in ticks, blood digestion is accompanied by the formation of huge endosomes that serve as places of storage and sorting of ingested material. Digestive cells show different types of endocytotic activity as well as various late endosomes, which implies different subcellular pathways for different blood components. In both midgut regions, elimination of the excretory material occurs by apocrine secretion or by discharging of apical cell fragments (loaded with lysosomes) into the gut lumen. The formation of guanine granules occurs inside the lysosomes of PMG epithelial cells thus having much in common with intracellular digestion. Peculiarities of intracellular blood digestion were analyzed according to the modern hypothesis of endocytosis and compared to what is known in ticks.     

UDP-glucose: Glucan Synthetase in Developing Cotton Fibers: II. Structure of the Reaction Product

The solubility properties, composition, and structure of the radioactive product synthesized from UDP-[¹⁴C]glucose by a highly active cotton fiber glucan synthetase have been determined. Product obtained under the following three different conditions was analyzed: at high and low substrate concentrations by detached fibers, and at high substrate concentrations with an isolated particulate preparation. The results of acetic and nitric acid digestion, enzyme digestion, total acid hydrolyses, periodate oxidation, partial acid hydrolyses, and methylation analyses all support the conclusion that the product of the glucan synthetase produced under all three assay conditions is a linear β-(1→3)-glucan.     

Poly(adenosine diphosphate ribose) metabolism and regulation of myocardial cell growth by oxygen

Control of the rate of cardiac cell division by oxygen occurs most probably by altering the redox state of a control substance, e.g. NAD(+)right harpoon over left harpoonNADH. NAD(+) (and not NADH) forms poly(ADP-ribose), an inhibitor of DNA synthesis, in a reaction catalysed by poly(ADP-ribose) polymerase. Lower partial pressure of oxygen, which increases the rate of division, would shift NAD(+)-->NADH, decrease poly(ADP-ribose) synthesis, and increase DNA synthesis. Chick-embryo heart cells grown in culture in 20% O(2) (in which they divide more slowly than in 5% O(2)) did exhibit greater poly(ADP-ribose) polymerase activity (+83%, P<0.001) than when grown in 5% O(2). Reaction product was identified as poly(ADP-ribose) by its insensitivity to deoxyribonuclease, ribonuclease, NAD glycohydrolase, Pronase, trypsin and micrococcal nuclease, and by its complete digestion with snake-venom phosphodiesterase to phosphoribosyl-AMP and AMP. Isolation of these digestion products by Dowex 1 (formate form) column chromatography and paper chromatography allowed calculation of average poly(ADP-ribose) chain length, which was 15-26% greater in 20% than in 5% O(2). Thus in 20% O(2) the increase in poly(ADP-ribose) formation results from chain elongation. Formation of new chains also occurs, probably to an even greater degree than chain elongation. Additionally, poly(ADP-ribose) polymerase has very different K(m) and V(max.) values and pH optima in 20% and 5% O(2). These data suggest that poly(ADP-ribose) metabolism participates in the regulation of heart-cell division by O(2), probably by several different mechanisms.     

Ultrastructural changes in the gastrodermal phagocytic cells of the planarian Dugesia gonocephala s.l. during food digestion (Plathelminthes)

Summary In the present report the functional morphology of the planarian gastrodermal phagocytic cells is examined in feeding animals. A functional interpretation of some of the morphological findings is given. The events in the fine-structure modifications of the phagocytic cells in the course of phagocytosis and intracellular digestion of food particles were followed through five post-feeding stages in the planarian Dugesia gonocephala. Light and electron microscopical observations demonstrate that there is preliminary intraluminal digestion of food particles; their phagocytosis takes place quickly.Beef hepatocytes that served as food are found engulfed at first in food vacuoles near the apical border of the phagocytic cells, and are clearly recognizable. The vacuoles increase in number to occupy most of the cytoplasm of these cells. Progressive breakdown and disappearance of phagocytosed hepatocytes occurs. In time the vacuoles move deeper into the cells, their contents lose their identity, and condense to homogeneous or heterogeneous residual bodies. These are returned to the distal surface of the cells, and then voided into the intestinal lumen. At the same time, synthesis and accumulation of numerous lipid droplets occurs, probably as a final product resulting from metabolism of the digested material. When feeding is over, the phagocytic cells are filled with lipid droplets, acquiring their typical appearance.It is suggested that disintegration of phagocytic cells during starvation is balanced by proliferation and differentiation of neoblasts into new phagocytic cells during the feeding-starvation cycle.     

The handling of the mechanistic probe 5-fluorouridine by the pseudouridine synthase TruA and its consistency with the handling of the same probe by the pseudouridine synthases TruB and RluA

RNA containing 5-fluorouridine (F(5)U) had previously been used to examine the mechanism of the pseudouridine synthase TruA, formerly known as pseudouridine synthase I [Gu et al. (1999) Proc. Natl. Acad. Sci. U.S.A. 96, 14270-14275]. From that work, it was reasonably concluded that the pseudouridine synthases proceed via a mechanism involving a Michael addition by an active site aspartic acid residue to the pyrimidine ring of uridine or F(5)U. Those conclusions rested on the assumption that the hydrate of F(5)U was obtained after digestion of the product RNA and that hydration resulted from hydrolysis of the ester intermediate between the aspartic acid residue and F(5)U. As reported here, (18)O labeling definitively demonstrates that ester hydrolysis does not give rise to the observed hydrated product and that digestion generates not the expected mononucleoside product but rather a dinucleotide between a hydrated isomer of F(5)U and the following nucleoside in RNA. The discovery that digestion products are dinucleotides accounts for the previously puzzling differences in the isolated products obtained following the action of the pseudouridine synthases TruB and RluA on F(5)U in RNA.     

A simple ligation-based method to increase the information density in sequencing reactions used to deconvolute nucleic acid selections

Herein, a method is described to increase the information density of sequencing experiments used to deconvolute nucleic acid selections. The method is facile and should be applicable to any selection experiment. A critical feature of this method is the use of biotinylated primers to amplify and encode a BamHI restriction site on both ends of a PCR product. After amplification, the PCR reaction is captured onto streptavidin resin, washed, and digested directly on the resin. Resin-based digestion affords clean product that is devoid of partially digested products and unincorporated PCR primers. The product's complementary ends are annealed and ligated together with T4 DNA ligase. Analysis of ligation products shows formation of concatemers of different length and little detectable monomer. Sequencing results produced data that routinely contained three to four copies of the library. This method allows for more efficient formulation of structure-activity relationships since multiple active sequences are identified from a single clone.     

Protein distribution amongst chromatin particles following DNAse II digestion

When active chromatin is released as a Mg-soluble fraction following digestion of nuclei with DNAse II, as concomitant release of HMG proteins, and hnRNP particles occurs. Release of HMG 14 and 17 is dependent on active chromatin release, whereas HMG 1 and 2, and hnRNP particles are released in an independent process. The Mg-soluble fraction comprises a heterogenous mixture of particles of less compact conformation than normal nucleosomes, and prone to protein-induced aggregation. Histone H1, and HMG 14 and 17 appear to be associated with these particles in a reversible manner, whereas HMG 1 and 2 are unbound.     

An acetylenic mechanism-based inhibitor of dopamine beta-hydroxylase

The catalytic action of dopamine beta-hydroxylase on 1-phenyl-1-propyne results in concomitant loss of enzyme activity. At pH 5.5 and 25 degrees C, 1-phenyl-1-propyne inactivates dopamine beta-hydroxylase in a mechanism-based fashion. The inactivation rate is first-order, follows saturation kinetics, and is strictly dependent on catalysis (oxygen and ascorbate are essential). The inactivation rate of saturating 1-phenyl-1-propyne (kinact) increases from 0.08 to 0.22 min-1 when the oxygen saturation increases from 21 to 100%, respectively. Inactivation also requires a copper-containing catalytically competent enzyme. Tyramine and norepinephrine (respectively, substrate and product of the normal catalytic reaction) protect against inactivation, and no regain of enzyme activity occurs after prolonged dialysis. Experiments with ether-extracted incubation solutions (+/- enzyme) showed no difference in their gas chromatography-mass spectral patterns implying that inactivation of dopamine beta-hydroxylase by 1-phenyl-1-propyne occurs through a kinetic process with a partition ratio (kcat/kinact) equal to or near 1. Thus, this acetylenic substrate analog appears to be a very efficient mechanism-based inhibitor of dopamine beta-hydroxylase. We propose that inactivation of this enzyme by 1-phenyl-1-propyne proceeds by formation of a reactive intermediate that occurs prior to product formation and that alkylates an amino acid residue at the active site of the enzyme.     

Metabolic response to feeding in Tupinambis merianae: circadian rhythm and a possible respiratory constraint

The diurnal tegu lizard Tupinambis merianae exhibits a marked circadian variation in metabolism that is characterized by the significant increase in metabolism during part of the day. These increases in metabolic rate, found in the fasting animal, are absent during the first 2 d after meal ingestion but reappear subsequently, and the daily increase in metabolic rate is added to the increase in metabolic rate caused by digestion. During the first 2 d after feeding, priority is given to digestion, while on the third and following days, the metabolic demands are clearly added to each other. This response seems to be a regulated response of the animal, which becomes less active after food ingestion, rather than an inability of the respiratory system to support simultaneous demands at the beginning of digestion. The body cavity of Tupinambis is divided into two compartments by a posthepatic septum (PHS). Animals that had their PHS surgically removed showed no significant alteration in the postprandial metabolic response compared to tegus with intact PHS. The maximal metabolic increment during digestion, the relative cost of meal digestion, and the duration of the process were virtually unaffected by the removal of the PHS.     

Proteolytic processing of native Cry1Ab toxin by midgut extracts and purified trypsins from the Mediterranean corn borer Sesamia nonagrioides

The proteolytic processing of native Cry1Ab toxin by midgut extracts from the Mediterranean corn borer, Sesamia nonagrioides, takes place in successive steps. Several cuts occur until a 74 kDa protein is obtained; this is further digested to give rise to an active form of 69 kDa, which can be again processed to fragments of 67, 66 and 43 kDa. We have shown that three different trypsins (TI, TIIA and TIII) purified from the S. nonagrioides midgut were able to digest Cry1Ab protoxin to obtain the active form of 69 kDa. Interestingly, TI and TIII further hydrolyzed the 69 kDa protein to a fragment of slightly lower molecular mass (67 kDa), while TIIA was able to continue digestion to give fragments of 46 and 43 kDa. These results contrast with those obtained using bovine trypsin, in which the main product of Cry1Ab digestion is a 69 kDa protein. The digestion of the toxin with a "non-trypsin" fraction from S. nonagrioides midgut lumen, mostly containing chymotrypsins and elastases and free of trypsin-like activity, resulted in a different processing pattern, yielding fragments of 79, 77, 71, 69 and 51 kDa. Our results indicate that trypsins and other proteases are involved in the first steps of protoxin processing, but trypsins play the most important role in obtaining the 74 and 69 kDa proteins. All the digestion products, including the proteins of 46 and 43 kDa obtained from the digestion of Cry1Ab by TIIA, were toxic to neonate larvae, indicating that none of the tested proteases contribute to toxin degradation in a significant manner.     

Isolation of the globular region of the subcomponent q of the C1 component of complement.

Digestion after heat treatment of the subcomponent q of the C1 component of complement by collagenase leads to the isolation of the globular region of the protein. This product ('heads') is composed of three chains giving an overall molecular weight of about 57000. About half of the collagen-like region present in C1 q is lost after digestion. The 'heads' are shown to be soluble and hemolytically active products.     

Feeding and gut physiology in Acanthopleura spinigera (Mollusca)

The morphology and histology of the alimentary canal of the rock chiton Acanthopleura spinigera are described and the ability of regions of the gut to digest specific substrates investigated. The oesophagus is produced into a pair of thin-walled lateral pouches, the salivary glands or "sugar glands" which empty into the stomach. Folds of the capacious stomach are almost obscured by the large digestive gland over which is coiled the intestine. Histologically the gut consists of an outer layer of connective tissue, an inner muscular layer and a ciliated epithelium which varies in thickness from one region to the next. Proteases are most active in the stomach, digestive gland and anterior intestine at pH 6·5 and in the posterior intestine at pH 7·5-8·5. The digestion of lipoidal substance was greatest in the stomach and digestive gland and least in anterior intestine. There was little increase in the amount of digestion product obtained after 20 hours incubation. All regions of the alimentary canal and salivary gland were capable of digesting carbohydrates except that many low molecular weight carbohydrates were digested by salivary gland extracts only. The amylases were most active at pH 6–6·5. It is concluded that digestive enzymes are distributed throughout the intestinal tract but the amount of enzyme present varies from region to region, and is greatest just after feeding.     

Identification and quantification of Fc fusion peptibody degradations by limited proteolysis method

An Fc fusion protein expressed in Escherichia coli contains Met1 and Asp2 residues at the N terminus and an active peptide attached to the C terminus of the Fc region. Due to the unique amino acid sequence of Fc, many commonly used proteolysis methods have severe drawbacks for characterizing degradations of Met1 and Asp2 residues. A novel method has been developed to effectively characterize the degradations by employing a limited endoproteinase Glu-C digestion. The limited digestion generates a dimeric peptide of (Met1-Glu14)(2) due to specific cleavage at the residue Glu14 of the N terminus. This peptide together with its degraded products, including Met1 oxidation and Asp2 isomerization, can be identified and quantified by liquid chromatography-tandem mass spectrometry (LC-MS/MS). The optimization of digestion procedure and linearity of quantification are also described. This approach was successfully used in a photostability study to assess the product stability of an Fc fusion peptibody.