Relationship of the xeroderma pigmentosum group E DNA repair defect to the chromatin and DNA binding proteins UV-DDB and replication protein A

Cells from complementation groups A through G of the heritable sun-sensitive disorder xeroderma pigmentosum (XP) show defects in nucleotide excision repair of damaged DNA. Proteins representing groups A, B, C, D, F, and G are subunits of the core recognition and incision machinery of repair. XP group E (XP-E) is the mildest form of the disorder, and cells generally show about 50% of the normal repair level. We investigated two protein factors previously implicated in the XP-E defect, UV-damaged DNA binding protein (UV-DDB) and replication protein A (RPA). Three newly identified XP-E cell lines (XP23PV, XP25PV, and a line formerly classified as an XP variant) were defective in UV-DDB binding activity but had levels of RPA in the normal range. The XP-E cell extracts did not display a significant nucleotide excision repair defect in vitro, with either UV-irradiated DNA or a uniquely placed cisplatin lesion used as a substrate. Purified UV-DDB protein did not stimulate repair of naked DNA by DDB- XP-E cell extracts, but microinjection of the protein into DDB- XP-E cells could partially correct the repair defect. RPA stimulated repair in normal, XP-E, or complemented extracts from other XP groups, and so the effect of RPA was not specific for XP-E cell extracts. These data strengthen the connection between XP-E and UV-DDB. Coupled with previous results, the findings suggest that UV-DDB has a role in the repair of DNA in chromatin.     

A class of chromatin particles associated with nonhistone proteins

Unfixed nucleoproteins may be banded isopycnically in metrizamide (2(3-acetamido-5-N-methylacetamido-2,4,6-triiodobenzamido)-2-deoxy-D-glucose) according to the protein/nucleic acid ratio. Unsheared or lightly sheared chromatin bands sharply (p=1.2 g/ml); it has a protein/DNA ratio of 1.4. Chromatin sheared by sonication to approximately 350 base pairs of DNA contains two components with protein/nucleic acid ratios of approximately 1.3 (p=1,185 g/ml) and 2 (p=1.245 g/ml). When chromatin is digested exhaustively with staphylococcal nuclease, two density components are found, one with a protein/DNA ratio of 1.5 (p=1.21 g/ml), the other with a protein/DNA ratio of 2 (p=1.24 g/ml). In both instances the denser particle (p=1.24 g/ml) contains nearly all the nonhistone proteins, while both dense and light fractions contain histones in similar amounts. The base sequence complexity of DNA from the fractions is not distinguishable from that of total DNA and there is no evidence of any concentration of sequences complementary to polysomal polyadenylated RNA molecules.     

GPI-anchored complement regulatory proteins in seminal plasma. An analysis of their physical condition and the mechanisms of their binding to exogenous cells

We analyzed and compared the properties of three glycosylphosphatidylinositol (GPI)-anchored proteins. CD59, CD55 (both C regulators), and CDw52, and of the transmembrane C regulator CD46 in seminal plasma (SP). We demonstrated previously that anchor-intact SP CD59 is present on the membranes of vesicles (prostasomes) and that cells acquire this protein during incubation with SP. We now report that this acquisition is due partly to adherence of prostasomes to cells and partly to a second mechanism which may involve micellar intermediates. Using fluorescent labeling, ultracentrifugation, and density gradient centrifugation, virtually all CD46 was present on prostasomes whereas CD59, CD55, AND CDw52 were also detected in a form which remained in the 200,000 g supernatant and equilibrated at higher density than prostasomes in gradients. All three GPI-linked proteins eluted at high molecular mass during size exclusion chromatography of this nonprostasome fraction. As documented by videomicroscopy and biochemical analysis, cells acquired new copies of the GPI-linked proteins during incubation with the nonprostasome fraction as well as with prostasomes. These data demonstrate the presence in SP of a stable population of membrane-free, GPI-linked proteins available for transfer to cells. Binding of these proteins to spermatozoa and pathogens in SP may confer new properties on their membranes including increased resistance to C attack. Finally, our data raise the possibility that lipid-associated GPI-linked proteins may be suitable for therapeutic applications.     

Isolation from genomic DNA of sequences binding specific regulatory proteins by the acceleration of protein electrophoretic mobility upon DNA binding

To examine a role for the medullary nucleus paragigantocellularis (PGi) in mediation of the symptomatology of opioid withdrawal, bilateral electrical stimulation of the PGi was performed in conscious, unrestrained, opioid naive (nondependent) rats. A characteristic series of behaviors was elicited during each 30-min session of PGi stimulation. The profile of these behaviors resembled qualitatively, but was not quantitatively identical with those seen during precipitated withdrawal from opioid dependence. This behavioral syndrome has been termed, opioid withdrawal-like behavior. The opioid withdrawal-like behaviors were voltage-, but not frequency-, dependent. Tolerance to repeated stimulation of the PGi did not develop following a series of 30-min runs of stimulation over 3.5 h. Intracerebroventricular (i.c.v.) injections of the nonselective opioid antagonist, naloxone, significantly decreased (by 40-50%) the intensity of stimulation-induced behavioral responses, as did injections of either the mu-selective (beta-funaltrexamine, beta-FNA) or the delta-selective (naltrindole, NTI) opioid antagonists. In contrast, similar i.c.v. injections of the kappa-selective antagonist, nor-binaltorphimine (nor-BNI), did not block behavioral responses to PGi stimulation. The results indicate that activation of the PGi by electrical stimulation can elicit behaviors similar to those observed during opioid withdrawal. Endogenous opioids, acting through mu- and delta-, but not kappa-opioid receptors, participate in mediating opioid withdrawal-like behaviors induced by PGi stimulation.     

Lectins as probes of chromatin structure. Binding of concanavalin A to purified rat liver chromatin

Concanavalin A (Con A) binds specifically to rat liver chromatin. The extent of binding is directly proportional to both chromatin and concanavalin A concentration. It is reversible and inhibited by specific sugars for which concanavalin A has a binding site. Scatchard analysis reveals the presence of one type of Con A-binding site, with an apparent dissociation constant of 3 X 10(-7) M. A maximum of 10 pmol of Con A binds to 10 microgram of chromatin, indicating an average of one binding site/1400 base pairs of DNA. To identify the polypeptide chains which contain Con A-binding sites, chromosomal proteins were separated by electrophoresis on polyacrylamide gels containing sodium dodecyl sulfate. Con A receptors were localized by incubating the gel in 125I-Con A and subsequent autoradiography. Three major polypeptide bands which bind Con A were identified among the nonhistone chromosomal proteins. The apparent molecular weights of these glycoproteins are 135,000, 125,000, and 69,000. We suggest that lectins may serve as probes for the study of the organization of specific components in chromatin.     

Calorimetric investigation of ethidium and netropsin binding to chicken erythrocyte chromatin

We have investigated the thermodynamic aspects of the ligand binding to chromatin, using isothermal titration calorimetry. Two classical DNA ligands were used: an intercalator, ethidium bromide, and a minor groove binder, netropsin. Stoichiometry, affinity constant, and thermodynamic parameters were determined at various salt concentrations and different temperatures. The effect of ionic strength was analyzed according to the Record theory applied to chromatin. We also compared the binding parameters on naked DNA, H1/H5-depleted chromatin, and chromatin. We demonstrated that the presence of histones on DNA still allows the ligand binding that takes place according to a simple one single-site model. For both ligand types, the thermodynamic driving force is enthalpic and the association is characterized by a somewhat weaker affinity and more scattered ligand distribution than on naked DNA. The ligand affinity is weakly altered by the salt-induced compaction of the chromatin and the binding is accompanied by a release of one counterion per ligand molecule. The temperature-dependent studies revealed the existence of a small heat capacity change associated with ligand binding to chromatin, together with an enthalpy-entropy compensation that maintains the free energy constant over the investigated temperature range.     

Evidence for the covalent binding of hydroxyethyl radicals to rat liver microsomal proteins

It is well known that acetaldehyde is capable of covalent binding to liver proteins. However, in experiments using liver microsomes prepared from chronically ethanol-fed rats we have observed that the addition of EDTA-iron complex to the microsomes increases by about 4-5 fold both the spin trapping of hydroxyethyl radicals and the covalent binding of 14C-ethanol to proteins, while it only doubles acetaldehyde formation. Conversely, the presence of GSH strongly decreases the trapping of hydroxyethyl radicals and completely inhibits the covalent binding, without affecting acetaldehyde production. Furthermore, the spin trapping agent 4-pyridyl-N-oxide-t-butyl nitrone (4-POBN), previously employed for the detection of hydroxyethyl radicals, decreases by about 70% the covalent binding of 14C-ethanol to microsomal proteins. 4-POBN does not affect acetaldehyde production by liver microsomes, nor does it interfere with the covalent binding of acetaldehyde produced by ADH-mediated oxidation of ethanol. The results obtained indicate that hydroxyethyl radicals generated during ethanol oxidation by cytochrome P-450 play an important role in the alkylation of microsomal proteins consequent to ethanol metabolism.     

The diverse world of coenzyme A binding proteins

Coenzyme A is involved in a number of important metabolic pathways. Recently the structures of several coenzyme A binding proteins have been determined. We compare in some detail the structures of seven different coenzyme A protein complexes. These seven proteins all have distinctly different folds.     

Nucleosome dynamics. III. Histone tail-dependent fluctuation of nucleosomes between open and closed DNA conformations. Implications for chromatin dynamics and the linking number paradox. A relaxation study of mononucleosomes on DNA minicircles

The mean linking number () of the topoisomer equilibrium distribution obtained upon relaxation of DNA minicircles with topoisomerase I did not increase linearly, but rather in a step wise fashion, with DNA size between 351 and 366 bp. As a consequence, the corresponding linking number difference () did not remain equal to 0, but rather oscillated between +/-0.3 with the periodicity of the double helix. This oscillation, not observed with plasmid-size DNA, is an expected consequence of the stiffness of short DNA. When minicircles were reconstituted with a nucleosome, the associated oscillated between approximately -1.4 +/-0. 2. This oscillation appears to result from the combined effects of DNA stiffness, and nucleosome ability to thermally fluctuate between three distinct DNA conformational states. Two of these states, a closed approximately 1.75-turn DNA conformation with negatively crossed entering and exiting DNAs, and an open approximately 1.4-turn conformation with uncrossed DNAs, are well known, whereas the third state, with a closed DNA conformation and DNAs tending to cross positively rather than negatively, is less familiar. Access to both closed "negative" and "positive" states appears to be mediated by histone N-terminal tails, as shown by specific alterations to the oscillation caused by histone acetylation and phosphate ions, a potent tail destabilizator. These results extend previous observations of ethidium bromide fluorescence titration in the accompanying article, which have pointed to an histone tail-dependent flexibility of entering and exiting DNAs to positive crossing. They also show that DNA wrapping around the histones occurred without twist alteration compared to the DNA free in solution, and reveal an intriguing new facet of the "linking-number-paradox" problem: the possibility for linkers in chromatin to adopt different crossing status within an overall dynamic equilibrium which may be regulated by histone acetylation.     

Histone modification governs the cell cycle regulation of a replication-independent chromatin assembly pathway in Saccharomyces cerevisiae

We describe a replication-independent, cell cycle-regulated chromatin assembly pathway in budding yeast. The activity of this pathway is low in S phase extracts but is very high in G2, M, and G1 cell extracts, with peak activity in late M/early G1. The cell cycle regulation of this pathway requires a specific pattern of posttranslational modification of histones H3 and/or H4, which is distinct for H3/H4 present in S phase versus M and G1 phase cell extracts. Histone H3/H4 modification is therefore important for the reciprocal control of replication-dependent and -independent chromatin assembly pathways during the cell cycle.     

Exercise-induced overexpression of key regulatory proteins involved in glucose uptake and metabolism in tetraplegic persons: molecular mechanism for improved glucose homeostasis

Complete spinal cord lesion leads to profound metabolic abnormalities and striking changes in muscle morphology. Here we assess the effects of electrically stimulated leg cycling (ESLC) on whole body insulin sensitivity, skeletal muscle glucose metabolism, and muscle fiber morphology in five tetraplegic subjects with complete C5-C7 lesions. Physical training (seven ESLC sessions/wk for 8 wk) increased whole body insulin-stimulated glucose uptake by 33+/-13%, concomitant with a 2.1-fold increase in insulin-stimulated (100 microU/ml) 3-O-methylglucose transport in isolated vastus lateralis muscle. Physical training led to a marked increase in protein expression of GLUT4 (378+/-85%), glycogen synthase (526+/-146%), and hexokinase II (204+/-47%) in vastus lateralis muscle, whereas phosphofructokinase expression (282+/-97%) was not significantly changed. Hexokinase II activity was significantly increased, whereas activity of phosphofructokinase, glycogen synthase, and citrate synthase was not changed after training. Muscle fiber type distribution and fiber area were markedly altered compared to able-bodied subjects before ESLC training, with no change noted in either parameter after ECSL training. In conclusion, muscle contraction improves insulin action on whole body and cellular glucose uptake in cervical cord-injured persons through a major increase in protein expression of key genes involved in the regulation of glucose metabolism. Furthermore, improvements in insulin action on glucose metabolism are independent of changes in muscle fiber type distribution.