Biochemical characterization of the ribosomal decoding site

Prior to the emergence of crystal structures of the ribosome, different ribosomal functions were identified with specific regions of ribosomal RNA by biochemical and genetic approaches. In particular, three universally conserved bases of 16S rRNA, G530, A1492 and A1493, were implicated in the interaction of the incoming aminoacyl-tRNA with the 30S subunit and mRNA. The conserved region surrounding A1492 and A1493 was called the "decoding site", based on the results of chemical probing experiments and antibiotic resistance mutations. Crystallographic studies from the Ramakrishnan laboratory have now shown that G530 loop, A1492 and A1493 undergo localized conformational changes to form an RNA structure that positions these three bases to inspect the accuracy of the codon-anticodon match with high stereochemical precision, using A-minor interactions. Some results from the pre-X-ray era may provide clues to further aspects of the decoding process.     

Biochemical characterization of membrane fractions in murine sperm: Identification of three distinct sub‐types of membrane rafts

Despite enormous interest in membrane raft micro‐domains, no studies in any cell type have defined the relative compositions of the raft fractions on the basis of their major components—sterols, phospholipids, and proteins—or additional raft‐associating lipids such as the ganglioside, G_M1. Our previous localization data in live sperm showed that the plasma membrane overlying the acrosome represents a stabilized platform enriched in G_M1 and sterols. These findings, along with the physiological requirement for sterol efflux for sperm to function, prompted us to characterize sperm membrane fractions biochemically. After confirming limitations of commonly used detergent‐based approaches, we utilized a non‐detergent‐based method, separating membrane fractions that were reproducibly distinct based on sterol, G_M1, phospholipid, and protein compositions (both mass amounts and molar ratios). Based on fraction buoyancy and biochemical composition, we identified at least three highly reproducible sub‐types of membrane raft. Electron microscopy revealed that raft fractions were free of visible contaminants and were separated by buoyancy rather than morphology. Quantitative proteomic comparisons and fluorescence localization of lipids suggested that different organelles contributed differentially to individual raft sub‐types, but that multiple membrane micro‐domain sub‐types could exist within individual domains. This has important implications for scaffolding functions broadly associated with rafts. Most importantly, we show that the common practice of characterizing membrane domains as either “raft” or “non‐raft” oversimplifies the actual biochemical complexity of cellular membranes. J. Cell. Physiol. 218: 537–548, 2009. © 2008 Wiley‐Liss, Inc.     

Cell fractions from rat rib growth cartilage. Biochemical characterization of matrix molecules

In an attempt to isolate and characterize the putative target cells for growth hormone, chondrocytes were isolated from rat rib growth cartilage and fractionated by centrifugation in a discontinuous Percoll gradient. This resulted in three cell fractions with differing properties. The fraction with the lowest density consisted mainly of large, lipid-containing cells which became flattened in subsequent culture. The cells in this fraction were fair collagen producers but synthesized only minor amounts of proteoglycans and apparently no proteoglycan aggregates. These cells probably originate in the hypertrophy zone of the growth plate. The fraction with highest density, on the other hand, consisted of small cells which upon cell culture became polygonal and surrounded with refractile matrix. They synthesized less collagen, but more proteoglycans than the low-density fraction. The proportion of proteoglycan aggregates was rather low (10-20%) but otherwise the proteoglycans were similar to those synthesized by other chondrocytes. This cell fraction was tentatively identified as cells from the upper part of the growth plate. Finally, the middle fraction was heterogeneous, consisting of cells of varying shape. This fraction synthesized large amounts of both collagen and proteoglycans. In all three cell fractions, type II collagen predominated. There were also minor amounts of (1a, 2a, 3a) collagen, and, in the two denser fractions, of type I collagen.     

Biochemical characterization of chromatin fractions isolated from induced and uninduced friend erythroleukemia cells

Summary Chromatin fractions from Friend erythroleukemia cells after induction of differentiation by dimethylsulfoxide (DMSO) were compared in their biochemical characteristics to fractions from uninduced cells. Fractions were prepared by extracting chromatin from nuclei after mild micrococcal nuclease treatment with increasing concentrations of NaCl according to Sanders [1]. This procedure has been found to release chromatin containing hyperacetylated histones preferentially [2]. The fractions obtained by this procedure were analysed in respect to the amount of chromatin released, the amount of histone H1, the degree of acetylation of histone H4, the presence of non-histone proteins and the concentration of transcribed and non-transcribed sequences. It was found that the fractions differ in the amount of histone H1 present, in several non-histone proteins and in the acetylation of histonie H4, regardless whether induced or uninduced cells were analysed. The distribution of transcribed sequences versus non-transcribed sequences among the fractions was the same, demonstrating that this fractionation procedure, although leading to fractions with biochemical differences, is not able to discriminate functional states of chromatin and that the biochemical characteristics of the fractions may be common to both, active as well as inactive states of chromatin.     

Biochemical characterization of the catalytic domains of three different Clostridial collagenases

Clostridial collagenases are used for a broad spectrum of biotechnological applications and represent prime target candidates for both therapy and diagnosis of clostridial infections. In this study, we biochemically characterized the catalytic domains of three clostridial collagenases, collagenase G (ColG) and H (ColH) from Clostridium histolyticum, and collagenase T (ColT) from C. tetani. All protein samples showed activity against a synthetic peptidic substrate (furylacryloyl-Leu-Gly-Pro-Ala, FALGPA) with ColH showing the highest overall activity and highest substrate affinity. Whereas the K(m) values of all three enzymes were within the same order of magnitude, the turnover rate k(cat) of ColG decreased 50- to 150-fold when compared to ColT and ColH. It is noteworthy that the protein N-terminus significantly impacts their substrate affinity and substrate turnover as well as their inhibition profile with 1,10-phenanthroline. These findings were complemented with the discovery of a strictly conserved double-glycine motif, positioned 28 amino acids upstream of the HEXXH zinc binding site, which is critical for enzymatic activity. These observations have consequences with respect to the topology of the N-terminus relative to the active site as well as possible activation mechanisms.     

Simultaneous isolation of two platelet membrane fractions: Biochemical,immunological and functional characterization

Simultaneous isolation of two platelet membrane subfractions was achieved by centrifugation on 40 % sucrose from a 100.000g crude membrane fraction. Characterization of both types of membranes was carried out by different biochemical and immunological markers. Using a surface label, ³H Concanavaline A (³HCon A), a marker enzyme, phosphodiesterase, and lipid analysis, one of the fraction has been identified as external or plasma membranes, the other consists of intracellular membranes. Further two specific antibodies directed against external membrane antigens (LeK^a and LgG L) react almost exclusively with the external membranes. Finally both kinds of membranes were able to uptake calcium but the affinity for this cation was higher for the internal than for the external membranes. This suggests that both membranes are implicated in the regulation of the cytoplasmic calcium concentration and that the internal membranes (dense tubular system) play the major part in this regulation.     

Biochemical characterization of three nucleopolyhedrovirus isolates of Spodoptera exigua and Mamestra brassicae

Three nucleopolyhedroviruses (NPVs), of different geographical origins, were biochemically characterized and compared. Two that were isolated from Spodoptera exigua (Se-UZB and Se-SP3) in Uzbekistan and Spain were SeMNPV type, and the third which was isolated from Mamestra brassicae (Mb-PL) in Poland was MbMNPV type. The Spanish isolate Se-SP3 showed restriction endonuclease (REN) profiles that were closely related to two previously described Spanish strains Se-SP1 and Se-SP2, but had some unique and characteristic REN fragments. On the other hand, comparison between the Uzbekian (Se-UZB) and the Spanish (Se-SP1, Se-SP2, and Se-SP3) isolates from S. exigua showed unrelated REN profiles. However, the Pst I and Bgl II profiles of Se-UZB and Mb-PL were identical, and very similar to the REN profiles of the MbMNPV strain, which constitutes the active component of Mamestrin^® (NPP, Nagueres, France), a commercial bioinsecticide. It is therefore very likely that the Se-UZB samples were cross-infected by the Polish strain (Mb-PL). This work presents two new strains of SeMNPV and MbMNPV, called Se-SP3 and Mb-PL, respectively, which were surveyed in two distant areas.     

Biochemical characterization of three hamster melanoma variants--II. Glycolysis and oxygen consumption

Lactate production and oxygen consumption were studied in single cell suspension prepared from solid tumours of the black-melanotic (Ma), brown-melanotic (MI) and amelanotic (Ab) melanomas of hamster. Aerobic lactase production was about 5 times higher in the fast growing Ab melanoma than in the slow growing Ma and MI melanomas. Aerobic lactate production in both melanotic hamster melanomas was stimulated by 3-(3,4-dihydroxyphenyl)-L-alanine. This compound was without effect on the cells isolated from amelanotic hamster melanoma. L-Phenylalanine, a known competitive tyrosinase inhibitor reduced the stimulatory effect of L-DOPA on the the lactate production. Oxygen consumption was similar in all three melanomas. The oxygen consumption was inhibited completely by 1 mM potassium cyanide in the Ab melanoma but only in about 1/3 in the Ma and MI melanomas. The Pasteur effect was higher in relative terms and lower in absolute terms in the melanotic melanomas than in the Ab melanoma only . The Crabtree effect was present in the Ab melanoma only. Thus glycolysis measured by aerobic and anaerobic lactic acid formation, and cell respiration, measured by oxygen consumption sensitive to KCN, were both higher in the more malignant, less differentiated Ab melanoma than in the Ma and MI melanomas. The suggestion is presented that the process of melanogenesis influences both aerobic glycolysis and the KCN insensitive consumption in the melanotic hamster melanomas.     

Biochemical and molecular characterization of three barley seed proteins with antifungal properties

We have purified three proteins from barley (Hordeum vulgare L.) seeds which synergistically inhibit the growth of fungi measured in a microtiter well assay. The proteins are a 26-kDa chitinase, a 30-kDa ribosome-inactivating protein, and a 32-kDa (1-3)-beta-glucanase. Full-length cDNAs encoding them were isolated and sequenced to determine the complete primary structures of the proteins. Northern hybridizations with the cDNAs as probes showed that the corresponding mRNAs accumulate differentially during seed development and germination. Chitinase mRNA accumulates to high levels in aleurone cells during late seed development and early germination, while high levels of mRNA encoding the ribosome-inactivating protein accumulate only in the starchy endosperm during late seed development. The glucanase mRNA accumulates to low levels during seed development and to higher levels in aleurone and seedling tissues during germination. Southern hybridizations showed that the three proteins are encoded by small families of three to eight genes. Their biological roles and potential use in genetic engineering studies are discussed.     

Biochemical, electrophoretic and immunological characterization of peroxisomal enzymes in three soybean organs

Biochemical, electrophoretic and immunological studies were made among peroxisomal enzymes in three organs of soybean [Glycine max (L.) Merr. cv. Centennial] to compare the enzyme distribution and characteristics of specialized peroxisomes in one species. Leaves, nodules and etiolated cotyledons were compared with regard to several enzymes localized solely in their peroxisomes: catalase (EC 1.11.1.6), malate synthase (EC 4.1.3.2), glycolate oxidase (EC 1.1.3.1), and urate oxidase (EC 1.7.3.3). Catalase activity was found in all tissue extracts. Electrophoresis on native polyacrylamide gels indicated that leaf catalase migrated more anodally than nodule or cotyledon catalase as shown by both activity staining and Western blotting. Malate synthase activity and immunologically detectable protein were present only in the cotyledon extracts. Western blots of denaturing (lithium dodecyl sulfate) gels probed with anti-cotton malate synthase antiserum, reveal a single subunit of 63 kDa in both cotton and soybean cotyledons. Glycolic acid oxidase activity was present in all three organs, but ca 20-fold lower (per mg protein) in both nodule and cotyledon extracts compared to leaf extracts. Electrophoresis followed by activity staining on native gels indicated one enzyme form with the same mobility in nodule, cotyledon and leaf preparations. Urate oxidase activity was found in nodule extracts only. Native gel electrophoresis showed a single band of activity. Novel electrophoretic systems had to be developed to resolve the urate oxidase and glycolate oxidase activities; both of these enzymes moved cathodally in the gel system employed while most other proteins moved anodally. This multifaceted study of enzymes located within three specialized types of peroxisomes in a single species has not been undertaken previously, and the results indicate that previous comparisons between the enzyme content of specialized peroxisomes from different organisms are mostly consistent with that for a single species, soybean.     

Biochemical and genetic characterization of three hamster cell mutants resistant to diphtheria toxin

We describe here three different hamster cell mutants which are resistant to diphtheria toxin and which provide models for investigating some of the functions required by the toxin inactivates elongation factor 2 (EF-2). Cell-free extracts from mutants Dtx(r)-3 was codominant. The evidence suggests that the codominant phenotype is the result of a mutation in a gene coding for EF-2. The recessive phenotype might arise by alteration of an enzyme which modifies the structure of EF-2 so that it becomes a substrate for reaction with the toxin. Another mutant, Dtx(r)-2, contained EF-2 that was sensitive to the toxin and this phenotype was recessive. Pseudomonas aeruginosa exotoxin is known to inactivate EF-2 as does diphtheria toxin and we tested the mutants for cross-resistance to pseudomonas exotoxin. Dtx(r)-1 and Dtx(r)-3 were cross-resistant while Dtx(r)-2 was not. It is known that diphtheria toxin does not penetrate to the cytoplasm of mouse cells and that these cell have a naturally occurring phenotype of diphtheria toxin resistance. We fused each of the mutants with mouse 3T3 cells and measured the resistance. We fused each of the mutants with mouse 3T3 cells and measured the resistance of the hybrid cells to diphtheria toxin. Intraspecies hybrids containing the genome of mutants Dtx(r)-1 and Dtx(r)-3 had some resistance while those formed with Dtx(r)-2 were as sensitive as hybrids derived from fusions between wild-type hamster cells and mouse 3T3 cells.     

Biochemical characterization of three hamster melanoma variants--I. Tyrosinase activity and melanin content

Tyrosinase activity in the soluble fraction of the cells and melanin content in the whole cells of the black-melanotic (Ma), brown-melanotic (MI) and amelanotic (Ab) hamster melanomas were studied. The activity of the soluble tyrosinase was highest in MI lower in Ma, and very low in Ab melanoma. Melanin content was greatest in the Ma, lower in MI, and none in Ab melanoma. Acrylamide gel electrophoretic pattern of the soluble tyrosinase consisted of 2 bands in Ma and MI melanomas, and of 1 band in Ab melanoma.     

Immunotherapy of a guinea pig hepatoma with vaccines containing mycobacterial fractions

Summary BCG cell walls (CW) were compared to trehalose-6,6-dimycolate (TDM) in admixture with endotoxin (ET) for their potency to cause regression of a transplanted guinea pig hepatoma. On a weight basis, CW were at least as active as ET-TDM. Toxicity of ET and of ET-TDM were greater than that of CW as judged by weight loss after intravenous administration to normal guinea pigs.     

Biochemical and physiochemical characterization of chromatin fractions with different degrees of solubility isolated from chicken erythrocyte nuclei

Chicken erythrocyte chromatin was prepared according to two different methods [Fulmer, A. W., & Bloomfield, V. A. (1981) Proc. Natl. Acad. Sci. U.S.A. 78, 5968-5972; Ausio, J., Borochov, N., Seger, D., & Eisenberg, H. (1984) J. Mol. Biol. 177, 373-398] to give three main common fractions, according to its solubility (S) or insolubility (I) in 0.15 M NaCl buffers or to its further solubility in 0.25 mM ethylenediaminetetraacetic acid (E). From the biochemical point of view, all of them have been found to be undistinguishable. Analytical ultracentrifugation shows that all of these fractions can reversibly undergo the transition from the low to the higher order structure, through a nearly identical way of folding. Thermal denaturation profiles yielded three transitions having the same Tm's for the three fractions. The percentage of DNA melting in the first transition decreased in the order S greater than I greater than E, and the amount in the second transition increased in the same order. Together with the different solubility of these fractions in the presence of divalent ions, these results indicate that in the three fractions of chromatin studied, the amount of linker DNA bound to the nucleosome varied.     

Preparation and characterization of membrane fractions enriched in outer and inner envelope membranes from spinach chloroplasts. II. Biochemical characterization

In the previous paper (Block, M. A., Dorne, A.-J., Joyard, J., and Douce, R. (1983) J. Biol. Chem. 258, 13273-13280), we have described a method for the separation of membrane fractions enriched in outer and inner envelope membranes from spinach chloroplasts. The two envelope membranes have a different weight ratio of acyl lipid to protein (2.5-3 for the outer envelope membrane and 0.8-1 for the inner envelope membrane). The two membranes also differ in their polar lipid composition. However, in order to prevent the functioning of the galactolipid:galactolipid galactosyltransferase during the course of envelope membrane separation, we have analyzed the polar lipid composition of each envelope membrane after thermolysin treatment of the intact chloroplasts. The outer envelope membrane is characterized by the presence of high amounts of phosphatidylcholine and digalactosyldiacylglycerol whereas the inner envelope membrane has a polar lipid composition almost identical with that of the thykaloids. No phosphatidylethanolamine or cardiolipin could be detected in either envelope membranes, thus demonstrating that the envelope membranes, and especially the outer membrane, do not resemble extrachloroplastic membranes. No striking differences were found in the fatty acid composition of the polar lipids from either the outer or the inner envelope membrane. The two envelope membranes also differ in their carotenoid composition. Among the different enzymatic activities associated with the chloroplast envelope, we have shown that the Mg2+-dependent ATPase, the UDP-Gal:diacylglycerol galactosyltransferase, the phosphatidic acid phosphatase, and the acyl-CoA thioesterase are associated with the inner envelope from spinach chloroplasts whereas the acyl-CoA synthetase is located on the outer envelope membrane.     

Purification and characterization of mycobacterial phospholipase A: an activity associated with mycobacterial cutinase

We describe mycobacterial phospholipase A activity (MPLA) and, using reverse genetics, have associated this activity with putative mycobacterial cutinase. PLAs, which hydrolyze fatty acids on phospholipids, play a significant role in human inflammatory states and disease pathogenesis. In prokaryotes, the recognition of their role in virulence is more recent. Cutinases are serine esterases whose primary substrate is cutin, the waxy exterior layer of plants. Mycobacterium tuberculosis has maintained seven putative cutinases, though it should not encounter cutin; we demonstrate that known cutinases and MPLA cleave phospholipids in a PLA-type manner and also hydrolyze Tween. We analyzed cutinase motifs in mycobacteria and found the motif very prevalent. All mycobacteria tested had MPLA activity. These studies suggest an alternative use for putative cutinases by the M. tuberculosis group that is likely related to MPLA activity and lipid metabolism.     

Distribution of newly formed ribosomal proteins in HeLa cell fractions

The distribution of newly formed ribosomal proteins between cytoplasmic, nucleoplasmic, and nucleolar fractions of HeLa cells was determined. All but a few of the newly formed ribosomal proteins were concentrated 10- to 50-fold in the nucleolus and two- to fivefold in the nucleoplasm. Nevertheless, substantial amounts were found in the cytoplasm. Pretreatment of cells with actinomycin D to deplete the nucleolar pool of ribosomal precursor RNA had no effect on the concentration of newly formed ribosomal proteins in the nucleus, but did lead to an increased amount in the nucleoplasm at the expense of the nucleolus.