CREB-binding protein (CBP)/p300 and RNA polymerase II colocalize in transcriptionally active domains in the nucleus.

The spatial organization of transcription- associated proteins is an important control mechanism of eukaryotic gene expression. Here we analyzed the nuclear distribution of the transcriptional coactivators CREB-binding protein (CBP)/p300 in situ by confocal laser scanning microscopy, and in vivo complex formation by coimmunoprecipitation. A subpopulation of CBP and p300 is targeted to active sites of transcription and partially colocalizes with hyper- and hypophosphorylated RNA polymerase II (pol II) in discrete regions of variable size throughout the nucleus. However, the coactivators were found in tight association with hypophosphorylated, but not hyperphosphorylated pol II. Transcriptional inhibition induced a relocation of CBP/p300 and pol II into speckles. Moreover, double and triple immunofluorescence analyses revealed the presence of CBP, p300, and pol II in a subset of promyelocytic leukemia (PML) bodies. Our results provide evidence for a dynamic spacial link between coactivators of transcription and the basal transcription machinery in discrete nuclear domains dependent upon the transcriptional activity of the cell. The identification of pol II in CBP/PML-containing nuclear bodies supports the idea that transcription takes place at PML bodies.

Isoform-specific increase of spastin stability by N-terminal missense variants including intragenic modifiers of SPG4 hereditary spastic paraplegia.

Hereditary spastic paraplegia (HSP) is a neurodegenerative disorder selectively affecting axons of spinal cord motoneurons. Classical mutations in the most frequent HSP gene SPAST (spastin protein) act through haploinsufficiency by abolishing the activity of a C-terminal ATPase domain or by interfering with expression from the affected allele. N-terminal missense variants have been suggested to represent rare polymorphisms, to cause unusually mild phenotypes, and to aggravate the effect of a classical mutation. We confirm these associations for p.S44L but do not detect two other variants (p.E43Q; p.P45Q) in HSP patients and controls. We show that neither of several disease mechanisms associated with classical SPAST mutations applies to the N-terminal variants. Instead, all three alterations enhance the stability of one of two alternative spastin isoforms. Their phenotypic effect may thus not be mediated by haploinsufficiency but by increasing isoform competition for interacting proteins, substrates or oligomerization partners.

Determination of the binding constants of the centromere protein Cbf1 to all 16 centromere DNAs of Saccharomyces cerevisiae.

Cbf1p is a Saccharomyces cerevisiae chromatin protein belonging to the basic region helix-loop-helix leucine zipper (bHLHzip) family of DNA binding proteins. Cbf1p binds to a conserved element in the 5'-flanking region of methionine biosynthetic genes and to centromere DNA element I (CDEI) of S.cerevisiae centromeric DNA. We have determined the apparent equilibrium dissociation constants of Cbf1p binding to all 16 CDEI DNAs in gel retardation assays. Binding constants of full-length Cbf1p vary between 1.7 and 3.8 nM. However, the dissociation constants of a Cbf1p deletion variant that has been shown to be fully sufficient for Cbf1p function in vivo vary in a range between 3.2 and 12 nM. In addition, native polyacrylamide gel electrophoresis revealed distinct changes in the 3D structure of the Cbf1p/CEN complexes. We also show that the previously reported DNA binding stimulation activity of the centromere protein p64 functions on both the Cbf1 full-length protein and a deletion variant containing only the bHLHzip domain of Cbf1p. Our results suggest that centromeric DNA outside the consensus CDEI sequence and interaction of Cbf1p with adjacent centromere proteins contribute to the complex formation between Cbf1p and CEN DNA.

Conserved Senescence Associated Genes and Pathways in Primary Human Fibroblasts Detected by RNA-Seq.

Cellular senescence correlates with changes in the transcriptome. To obtain a complete view on senescence-associated transcription networks and pathways, we assessed by deep RNA sequencing the transcriptomes of five of the most commonly used laboratory strains of human fibroblasts during their transition into senescence. In a number of cases, we verified the RNA-seq data by real-time PCR. By determining cellular protein levels we observed that the age-related expression of most but not all genes is regulated at the transcriptional level. We found that 78% of the age-affected differentially expressed genes were commonly regulated in the same direction (either up- or down-regulated) in all five fibroblast strains, indicating a strong conservation of age-associated changes in the transcriptome. KEGG pathway analyses confirmed up-regulation of the senescence-associated secretory phenotype and down-regulation of DNA synthesis/repair and most cell cycle pathways common in all five cell strains. Newly identified senescence-induced pathways include up-regulation of endocytotic/phagocytic pathways and down-regulation of the mRNA metabolism and the mRNA splicing pathways. Our results provide an unprecedented comprehensive and deep view into the individual and common transcriptome and pathway changes during the transition into of senescence of five human fibroblast cell strains.

Structure and properties of 5-deazaflavin radicals as compared to natural flavosemiquinones.

In order to gain more insight into flavin radicals, on which the selection of 1e-, and 2e- -oxireduction modes in flavoproteins depends, we have investigated structure, spectral properties and decay mode of molecular species occurring in the half-reduced 5-deazaflavin "model" system by flash photolysis and pulse radiolysis. (1) Enforced 1e- -reduction of 5-deazaflavin yields the short-lived red-colored 1-HdFl, which is a strong reductant. In the absence of any electron acceptor, this radical decays by 1,5-prototropy (see below) and dismutation, which is rapidly reversed upon illumination. Competing with this photo-comproportionation, irreversible formation of the photo-stable sigma-dimmer (HdFl)2, covalently linked via C(5), is observed, which becomes prevalent under prolonged illumination. (2) Enforced 1e- -abstraction from 1,5-dihydro-5-deazaflavin yields the tautomeric 5-HdFl, which is a mild oxidant and is transparent at lambda 480 nm. Prototropy 5-HdFl in equilibrium or formed from 1-HdFl can be rate-determining in 5-deazaflavin redox reactions. Hence, the radical state in the 5-deazaflavin system does not mediate double 1e- -oxidoreduction as do natural flavosemiquinones. Instead, 5-deazaflavin flavors nucleophilic substrate addition (carbanion transfer) and formation of intermediate sigma-adducts in (photo)reductions even over the extent observed with natural flavin. This confirms the description of 5-deazaflavin as a "flavin-shaped nicotinamide derivative". It explains at the same time the mechanism of 5-deazaflavin acting as a mild and yet potent photosensitizer in 1e- -reductions of biological redox systems. (3) It is shown that replacement of N(5) by CH in the flavin nucleus also leads to the disappearance of the known action-pK in the photoreduction, which confirms the assignment of the latter pK in the natural flavin system to 5-protonation of the excited flavin triplet. From these model studies the following biological conclusions can be confirmed: The tautomer equilibrium of natural flavin semiquinones is diffusion-controlled and regulated thermodynamically: 5-HFl in equilibrium or formed from 1-HFl, while in flavo-proteins the same equilibrium is regulated by regiospecific H-bridges from the apoprotein, which thus decides between 1e- - (stable 5-HFl) and 2e- -reaction (unstable 1-HFl) modes.

Characterization of eukaryotic protein L7 as a novel autoantigen which frequently elicits an immune response in patients suffering from systemic autoimmune disease.

Autoantibodies targeted against cellular proteins and nucleic acids are a common feature of autoimmune diseases. In this study, we show that ribosomal protein L7 is a novel autoantigen in patients suffering from systemic lupus erythematosus (SLE) and other connective tissue diseases. From 24 patients diagnosed as having SLE, 18 produce antibodies which precipitate in vitro translated L7 protein. The anti-L7 titer appears to correlate with the active state of the disease. Anti-L7 autoantibodies were also detected in 7 of 13 patients with mixed connective tissue disease (MCTD), 2 of 7 patients with rheumatoid arthritis (RA), 1 of 4 patients with Sjögren's syndrome (SS) and in 1 patient with progressive systemic sclerosis (PSS). Anti-L7 autoantibodies belong to the IgG-class and detect specifically at least two epitopes on the L7 molecule, as shown by immunoprecipitation and immunoblotting. The epitope(s) of the highly conserved C-terminal region are preferentially recognized. Utilizing rabbit anti-L7 serum, autoimmune sera and affinity-purified anti-L7 autoantibodies in immunoblotting, and rabbit and chicken anti-L7 antibodies in indirect immunofluorescence, we detect L7 protein in the nuclei and in the cytoplasm of various cell-lines. Yet unlike most integral structural components of ribosomes, L7 is absent from nucleoli.

On the environment and the rotational motion of amphiphilic flavins in artificial membrane vesicles as studied by electron paramagnetic resonance spectrometry.

This paper continues the studies of vesicle-bound flavins ('anisotropic flavin chemistry'). It is possible to anchor the flavin nucleus in various modes within the lipids/water interface by means of long aliphatic chains and using different saturated lipids, thereby mimicking the specific binding of the coenzyme to the apoprotein in flavoproteins. Based on absorption spectroscopy and EPR spectroscopy studies we explored the rotational mobility and the microenvironment of membrane-bound amphiflavin radicals. N(5)-unsubstituted amphiflavin radicals exhibit a similarly high disproportionation constant as known from isotropic flavin chemistry. However, reasonable stabilization of the radical was achieved by introduction of an alkyl group in position 5 in the reduced state prior to the one-electron oxidation. Adopting the fine structure of the corresponding EPR spectra as assay for the mobility of the semiquinone, we determined rotational relaxation times ranging from 60 ns in the crystalline state down to 10 or 15 ns in the liquid-crystalline state of the membrane. The solvatochromic effect shown by absorption spectra of the membrane-bound flavin radicals reflects a dielectric constant of the microenvironment of c = 30-40, corresponding to the lipid/water interface region. The results obtained in this study are consistent with those obtained previously, from fluorescence analyses, supporting our former conclusions.

Unexpected pathogenic mechanism of a novel mutation in the coding sequence of SPG4 (spastin).

The authors report a nucleotide substitution (c.1216A>G) in SPG4 (spastin) causing hereditary spastic paraplegia. This apparent missense mutation in the ATPase domain confers aberrant, in-frame splicing and results in destabilization of mutated transcript. Mutated protein is deficient in microtubule-severing activity but, unlike neighboring mutations, shows regular subcellular localization. The authors' data point to haploinsufficiency rather than a dominant negative effect as the disease-causing mechanism for this mutation.

Flavin-dependent substrate photo-oxidation as a chemical model of dehydrogenase action.

As a model of flavin-dependent biological dehydrogenation, flavin-sensitized photodehydrogenation and photodecarboxylation were studied by variation of substrate, flavin, pH and solvent. Evidence for the following rules is given. (1) When the reactive site of a photosubstrate is an alpha-carbon atom of the type CH-CO2-, decarboxylation is preferred over dehydrogenation, whereas the reverse is true for the neutral CH-CO2H. (2) Consequently these reactions do not exhibit a measurable isotope effect with C2H-CO2-, in contrast with the findings by Penzer, Radda, Taylor & Taylor [(1970) Vitam. Horm. (N.Y.) 28, 441--466], which could not be reproduced. When the substate does not contain a carboxylate group, isotope effects occur, in verification of previous reports, e.g. for benzyl alcohol C6H5-C2H20H. (3) The mechanism of flavin-sensitized substrate photodecarboxylation is assumed to consist in a primary carbanion fixation at the flavin nucleus (position 4a, 5 or 8) with concomitant liberation of CO2. This step is followed by rapid fragmentation of the adduct CH-Fl-red., provided that the substrate contains a functional and electron-donating group X, e.g. X = OH, OCH3 or NH2 (but not NH3+ !) in X CH-CO2-. (4) The minimal requirement for flavin-sensitized C-H dehydrogenation is the presence of a hydroxyl group. For example, methanol as substrate and solvent is dehydrogenated at pH sufficiently alkaline for detection of the presence of the active species CH3O-, whereas at more acidic pH substrate dehydrogenation is competing with flavin autophotolysis, which depends on the substituents in the flavin nucleus.

Photoreduction of flavoproteins and other biological compounds catalyzed by deazaflavins.

Deazaflavins have been found to act as potent catalysts in the photoreduction of flavoproteins in the presence of EDTA and other "photosubstrates". In distinction to the catalysis brought about by normal flavins which involves dark reaction of the photoreduced flavin catalyst, the mechanism of the catalysis by deazaflavins has been shown to involve unstable, strongly reducing radicals which are generated by photolysis of a preformed covalent dimer. By this new method it is possible to reduce not only flavoproteins but a variety of other redox proteins, including heme proteins and iron-sulfur proteins. By virtue of its great catalytic efficiency, it is possible to employ concentrations of deazaflavin sufficiently low as not to interfere with the spectral evaluation of the reduced proteins obtained.

Photodehalogenation of 7- and 8-halogen-substituted flavins. Photochemistry of the reduced flavin chromophore.

Flavodoxin was reconstituted with 8-chloro- and 7-bromo-FMN and p-hydroxybenzoate hydroxylase with the analogous FAD derivatives. In all cases, the spectral properties of the artificial enzymes changed as a result of photoreduction in the presence of ethylenediaminetetraacetate or oxalate as sources of reducing equivalents. The same changes were found to occur on irradiation of the enzymes which had been reduced previously in the dark under anaerobic conditions with dithionite. Using analogous 7- and 8-chlorolumiflavins, the observed changes were shown to be due to a novel photoreaction of the reduced flavin chromophore, in which either the 7- or 8-halogen substituent is eliminated and replaced by a proton derived from the solvent. The same reaction was shown to occur with 7,8-bis-norlumiflavin where 1 deuterium atom was incorporated into the molecule as a result of photoirradiation of the reduced flavin in deuterated medium. In the case of p-hydroxybenzoate hydroxylase, both the 8-chloro-FAD and 7-bromo-FAD enzymes, as well as their 8-nor-FAD and 7-nor-FAD photoproducts, possessed catalytic activity comparable to that of the native enzyme.

Antinuclear autoantibodies: fluorescent highlights on structure and function in the nucleus.

The eukaryotic nucleus is dynamically organized with respect to particular activities, such as RNA transcription, RNA processing or DNA replication. The spatial separation of metabolic activities is best reflected by the identification of functionally related proteins, in particular substructures of the nucleus. In a variety of human diseases, the integrity of such structures can be compromised, thus underlining the importance of a proper nuclear architecture for cell viability. Besides their clinical relevance, antinuclear autoantibodies (ANAs) have contributed to a large extent to the identification of subnuclear compartments, the isolation and cloning of their components (the autoantigens), as well a the characterization of their function. Although sophisticated techniques, such as confocal laser scanning microscopy (CLSM), fluorescence resonance energy transfer (FRET) and in vivo observation of cellular events have recently been established as valuable tools to study subnuclear architecture and function, cell biologists will continue to appreciate the specificity and power of ANAs for their research.

Light-mediated reduction of flavoproteins with flavins as catalysts.

It has been found that small amounts of free flavins greatly accelerate the photochemical reduction of flavoproteins both to the radical and fully reduced oxidation states. This catalytic effect has been shown to be due to the rapid photochemical reduction of the free flavin to its fully reduced state, followed by its reaction with the flavoprotein to yield flavoprotein radical and by its reaction with flavoprotein radical to yield fully reduced flavoprotein. Evidence is presented that the same route may occur with flavoproteins in the absence of added flavins. In this case the photoreduction is mediated by the small equilibrium concentration of free flavin coenzyme present in a flavorprotein solution. Hence, it is suggested that flavoprotein reduction with EDTA as photosubstrate does not involve an excited state of the holoprotein, nor contact of EDTA with the enzyme, but exchange of electrons between enzyme flavin and free reduced flavin.