RNF4 interacts with both SUMO and nucleosomes to promote the DNA damage response

The post‐translational modification of DNA repair and checkpoint proteins by ubiquitin and small ubiquitin‐like modifier (SUMO) critically orchestrates the DNA damage response (DDR). The ubiquitin ligase RNF4 integrates signaling by SUMO and ubiquitin, through its selective recognition and ubiquitination of SUMO‐modified proteins. Here, we define a key new determinant for target discrimination by RNF4, in addition to interaction with SUMO. We identify a nucleosome‐targeting motif within the RNF4 RING domain that can bind DNA and thereby enables RNF4 to selectively ubiquitinate nucleosomal histones. Furthermore, RNF4 nucleosome‐targeting is crucially required for the repair of TRF2‐depleted dysfunctional telomeres by 53BP1‐mediated non‐homologous end joining.     

Optical Rotatory Dispersion and Circular Dichroism of the Carboxyl Chromophore in Gibbane-10-carboxylic Acids with an Aromatic A Ring,and Their Application to the Stereochemistry of the B Ring of Gibberellins and Their Derivatives

CD and ORD of twelve gibbane-10-carboxylic acid compounds with an aromatic A ring together with two related compounds were measured. The sign of the Cotton effect was found to be positive (negative) when the configuration of the C–10 carboxyl is β (α). The ORD also provided information to determine the configuration at C–4b. The C–10 carboxyl gave a stronger magnitude and redshift of the peak in a cis relation with 4b–H compared with that in a trans relation.     

Ubiquitin-specific Protease 11 (USP11) Deubiquitinates Hybrid Small Ubiquitin-like Modifier (SUMO)-Ubiquitin Chains to Counteract RING Finger Protein 4 (RNF4)

Ring finger protein 4 (RNF4) is a SUMO-targeted ubiquitin E3 ligase with a pivotal function in the DNA damage response (DDR). SUMO interaction motifs (SIMs) in the N-terminal part of RNF4 tightly bind to SUMO polymers, and RNF4 can ubiquitinate these polymers in vitro. Using a proteomic approach, we identified the deubiquitinating enzyme ubiquitin-specific protease 11 (USP11), a known DDR-component, as a functional interactor of RNF4. USP11 can deubiquitinate hybrid SUMO-ubiquitin chains to counteract RNF4. SUMO-enriched nuclear bodies are stabilized by USP11, which functions downstream of RNF4 as a counterbalancing factor. In response to DNA damage induced by methyl methanesulfonate, USP11 could counteract RNF4 to inhibit the dissolution of nuclear bodies. Thus, we provide novel insight into cross-talk between ubiquitin and SUMO and uncover USP11 and RNF4 as a balanced SUMO-targeted ubiquitin ligase/protease pair with a role in the DDR.     

Replication of mitochondrial DNA occurs throughout the mitochondria of cultured human cells

Replication of mitochondrial DNA (mtDNA) is dependent on nuclear-encoded factors. It has been proposed that this reliance may exert spatial restrictions on the sites of mtDNA replication within the cytoplasm, as a previous study only detected mtDNA synthesis in perinuclear mitochondria. We have studied mtDNA replication in situ in a variety of human cell cultures labeled with 5-bromo-2'-deoxyuridine. In contrast to what has been reported, mtDNA synthesis was detected at multiple sites throughout the mitochondrial network following short pulses with bromodeoxyuridine. Although no bromodeoxyuridine incorporation was observed in anuclear platelets, incorporation into mtDNA of fibroblasts that had been enucleated 2 h prior to labeling was readily detectable. Blotting experiments indicated that the bromodeoxyuridine incorporation into mtDNA observed in situ represents replication of the entire mtDNA molecule. The studies also showed that replication of mtDNA occurred at any stage of the cell cycle in proliferating cells and continued in postmitotic cells, although at a lower level. These results demonstrate that mtDNA replication is not restricted to mitochondria in the proximity of the nucleus and imply that all components of the replication machinery are available at sufficient levels throughout the mitochondrial network to permit mtDNA replication throughout the cytoplasm.     

Preferential synthesis of plastid DNA and increased replication of plastids in cultured tobacco cells following medium renewal

During the culture of tobacco BY 2 cells derived from Nicotiana tabacum L. cv. Bright Yellow 2, morphological changes of plastid (pt) nucleoids and their replication were examined by fluorescence microscopy after staining with 46-diamidino-2-phenylindole. Upon transfer to fresh medium, the fluorescence intensity originating from pt nucleoids increased markedly. Copy numbers of ptDNA per cell calculated from the quantitative data by super-sensitive microspectroscopy increased 11-fold within 1 d of culture to reach 11 000, then decreased gradually to 1 000 after one week of culture. Autoradiography by labelling with [³H]thymidine showed that DNA synthesis in plastids occurred exclusively during the first day of culture, whereas nuclear DNA synthesis was observed from the first to the sixth day of culture. Replication of plastids was most frequently observed on the second day. Thereafter the formation of starch granules predominated in plastids up to the fifth day of culture, but the starch granules disappeared in the stationary-phase cells. The meaning of such preferential synthesis of ptDNA upon transfer to fresh medium is discussed in relation to the interaction between plastids and nuclei.Abbreviations pt plastid - DAPI 4,6-diamidino-2-phenylindole     

Dihydroxyacetone, the active browning ingredient in sunless tanning lotions, induces DNA damage, cell-cycle block and apoptosis in cultured HaCaT keratinocytes

Dihydroxyacetone (DHA), the active substance in sunless tanning lotions reacts with the amino groups of proteins to form a brown-colored complex. This non-enzymatic glycation, known as the Maillard reaction, can also occur with free amino groups in DNA, raising the possibility that DHA may be genotoxic. To address this issue we investigated the effects of DHA on cell survival and proliferation of a human keratinocyte cell line, HaCaT. Dose- and time-dependent morphological changes, chromatin condensation, cytoplasmic budding and cell detachment were seen in cells treated with DHA. Several dead cells were observed after long-time (24 h) incubation with 25 mM DHA or more. Furthermore, an extensive decline in proliferation was observed 1 day after DHA exposure for 24 h. When applied in different concentrations (5–50 mM) and for different time periods (1, 3 or 24 h) DHA caused a G₂/M block after the cyclin B₁ restriction point. Exit from this cell-cycle block was associated with massive apoptosis, as revealed by a clonogenic assay, TUNEL staining and electron microscopy. Furthermore, DHA caused DNA damage as revealed by the alkaline comet assay. Preincubation with antioxidants prevented the formation of DNA strand breaks. The DHA toxicity may be caused by direct redox reactions, with formation of ROS as the crucial intermediates. The genotoxic capacity of DHA raises a question about the long-term clinical consequences of treatment of the skin with this commonly used compound.     

Arabidopsis SKP1, a homologue of a cell cycle regulator gene, is predominantly expressed in meristematic cells

The yeast SKP1 gene and its human homolog p19 ^skp1 encode a kinetochore protein required for cell cycle progression at both the DNA synthesis and mitosis phases of the cell cycle. In orchids we identified a cDNA (O108) that is expressed in early stages of ovule development and is homologous to the yeast SKP1. Based on the orchid O108 cDNA clone, we identified and characterized an Arabidopsis thaliana (L.) Heynh. cDNA designated ATskp1 that also has high sequence similarity to yeast SKP1. The Arabidopsis ATskp1 is a single-copy gene that mapped to chromosome 1. The expression of the ATskp1 gene was highly correlated with meristem activity in that its mRNA accumulated in all of the plant meristems including the vegetative shoot meristem, inflorescence and floral meristems, root meristem, and in the leaf and floral organ primordia. In addition, ATskp1 was also highly expressed in the dividing cells of the developing embryo, and in other cells that become multinucleate or undergo endoreplication events such as the endosperm free nuclei, the tapetum and the endothelium. Based on its spatial pattern of expression, ATskp1 is a marker for cells undergoing division and may be required for meristem activity. Received: 6 June 1997 / Accepted: 2 July 1997     

Keeping the soma free of transposons: programmed DNA elimination in ciliates

Many transposon-related sequences are removed from the somatic macronucleus of ciliates during sexual reproduction. In the ciliate Tetrahymena, an RNAi-related mechanism produces small noncoding RNAs that induce heterochromatin formation, which is followed by DNA elimination. Because RNAi-related mechanisms repress transposon activities in a variety of eukaryotes, the DNA elimination mechanism of ciliates might have evolved from these types of transposon-silencing mechanisms. Nuclear dimorphism allows ciliates to identify any DNA that has invaded the germ-line micronucleus using small RNAs and a whole genome comparison of the micronucleus and the somatic macronucleus.     

Ribonuclease in plant vacuoles: purification and molecular properties of the enzyme from cultured tomato cells

A ribonuclease which was previously shown to be located in isolated vacuoles from suspension-cultured cells of tomato (Lycopersicon esculentum L.; Abel and Glund 1986, Physiol. Plant. 66, 79–86) has been purified to near homogeneity. Purification was up to 55000-fold with a yield of about 20%. The vacuolar origin of the protein was evidenced by comparing its electrophoretic mobility, isoelectric point, pH-optimum for activity and other properties with that of the RNA-degrading activity present in isolated vacuoles. The molecular weight of the native single polypeptide chain was estimated at 17500 and 20300 by gel filtration and sedimentation analysis, respectively. The enzyme hydrolyzed only single-stranded RNA with a mode of action that was endonucleolytic. The vacuolar ribonuclease had no requirement for divalent metal ions, and did not exhibit phosphomonoesterase (EC 3.1.3.1; EC 3.1.3.2) and phosphodiesterase (EC 3.1.15.1; EC 3.1.16.1) activity. The specificity of the enzyme has been studied by using homopolyribonucleotides as substrates. The end-products obtained were the respective nucleoside 2:3-cyclic monophosphates and, to minor extents, the corresponding nucleoside 3(2)-monophosphates. According to these observations, the vacuolar ribonuclease from tomato can be classified as ribonuclease I (EC 3.1.27.1).Abbreviations DEAE diethylaminoethyl - RNase ribonuclease - SDS-PAGE sodium dodecyl sulfate-polyacrylamide gel electrophoresis     

Qualitative and quantitative preservation of the fine structure of absorptive cells in cultured biopsies of human small-intestine

Summary The fine structure of the absorptive cells in human small-intestinal biopsies cultured for 6, 24, and 48 h was analyzed qualitatively and quantitatively. The findings show generally good preservation of the cultured absorptive cells and a normal distribution, size, and relative volume of their cell organelles, but there was a systematic decrease in the apical cell surface and an increase in the number of apical vesicles and tubules after culturing. Since the apical vesicles and tubules are thought to have a function in the transport of cell-coat material from the Golgi apparatus to the cell surface, these findings raise the question of whether a delayed transport or extrusion of cell surface material occurs.The diminished relative volume of the mitochondria and the increased signs of autophagy in some poorly preserved absorptive cells, are assumed to be an adaption to less favourable culture conditions.The authors acknowledge the help of Dr. A.S. Pena in the setting up of the organ culture technique, and also wish to thank Mrs. M.L. Bouwhuis for statistical advice and Mrs. M. de Gruil and Mr. L.D.C. Verschragen for technical assistance. The investigations were supported in part by the Foundation for Medical Research (FUNGO), which is subsidized by the Netherlands Organization for the Advancement of Pure Research (ZWO)     

Comparison of the intracellular pathways of immunoglobulin-G and low density lipoprotein in cultured human term trophoblast cells

Trophoblast cells were cultured on microporous membrane filters. After incubation at different times with gold-conjugated ligands, the cells were processed for electron microscopy. Gold particles indicating the presence of both IgG and LDL appeared in a time-dependent manner in coated pits and coated vesicles. LDL-gold appeared primarily within lysosomes whereas approximately 50% of the internalized IgG-gold appeared within vesicles (diameters ranging from 35 to 80 nm) near the basal regions of the cell. These vesicles may be the protective mechanism which prevents IgG breakdown during transcytosis across trophoblast cells, thus allowing transport of the intact molecule to the fetus.     

Liposome-mediated DNA transfer in eukaryotic cells: Dependence of the transfer efficiency upon the type of liposomes used and the host cell cycle stage

The pBR322 plasmid containing the sequence encoding β-lactamase, the enzyme conferring resistance to ampicillin, was encapsulated in liposomes of different phospholipid composition and incubated with synchronized cells. In mitotic cells as compared to cells synchronized in G₁, twice as many exogeneous DNA molecules were found associated with the cell nuclear DNA, when fluid, neutral liposomes were used. These liposomes are taken up by the cells mainly via endocytosis. When fluid, negatively charged liposomes were used as carriers about the same number of exogeneous DNA molecules were found associated with the nuclear DNA both in mitotic and in G₁-synchronized cells. The efficiency for gene transfer of liposomes entering the cells by different mechanisms was further studied and expressed both by the fraction of the radioactive plasmid associated with the nuclear DNA and by the level of the β-lactamase activity detected in the transfected cells. It appears that liposomes entering the cells mainly via an energy-dependent mechanism are more efficient for this type of DNA transfer.     

Activation of latent origins of DNA replication in florally determined shoot meristems of long-day and short-day plants: Silene coeli-rosa and Pharbitis nil

Replicon spacing was measured during the S-phase of the cell cycle in shoot meristems of Silene coeli-rosa L., a long-day (LD) plant, and Pharbitis nil Chois, a short-day (SD) plant to examine the hypothesis that activation of latent origins of DNA replication is a feature of floral determination. Silene coeli-rosa was germinated and grown in SD for 28 d and then exposed to either a florally inductive combination of 7 LD + 2 SD, the last day of which coincides with determination of the sepal and stamen whorls, or was germinated and grown in 37 non-inductive SD. Pharbitis nil was germinated and grown in continuous light (CL) for 5 d and then given either 48 h of inductive darkness followed by 1 d of CL, the last day of which coincides with determination of the sepal, petal and stamen whorls, or given one of two independent non-inductive treatments: 48 h dark interrupted by red light (R) + 1 d of CL, or 8 d of CL. Following these treatments, each batch of plants was exposed to tritiated [methyl-³H]thymidine for 30, 60, 90 or 120 min. Apical domes were dissected, nuclei lysed and prepared as fibre autoradiographs from which replicon size was recorded. In S. coeli-rosa, replicon size was in the range 10–15 μm in SD (non-inductive) and 0–5 μm in LD (inductive) while in P. nil it was 10–15 μm in the 48 h dark interrupted by R, 5–10 μm in CL (both non-inductive) but was reduced to 0–5 μm in the 48 h dark treatment (inductive). Therefore, the recruitment of additional initiation points for DNA replication occurred in both a LD and a SD plant immediately before the appearance of floral organs. The data are consistent in showing that a shortening of S-phase, which is a characteristic feature of florally determined shoot meristems for both species, is brought about by the activation of latent origins of DNA replication. Received: 14 May 1998 / Accepted: 20 August 1998     

Phosphorylation of Serine 51 Regulates the Interaction of Human DNA Ligase I with Replication Factor C and Its Participation in DNA Replication and Repair

Human DNA ligase I (hLigI) joins Okazaki fragments during DNA replication and completes excision repair via interactions with proliferating cell nuclear antigen and replication factor C (RFC). Unlike proliferating cell nuclear antigen, the interaction with RFC is regulated by hLigI phosphorylation. To identity of the site(s) involved in this regulation, we analyzed phosphorylated hLigI purified from insect cells by mass spectrometry. These results suggested that serine 51 phosphorylation negatively regulates the interaction with RFC. Therefore, we constructed versions of hLigI in which serine 51 was replaced with either alanine (hLigI51A) to prevent phosphorylation or aspartic acid (hLigI51D) to mimic phosphorylation. hLigI51D but not hLigI51A was defective in binding to purified RFC and in associating with RFC in cell extracts. Although DNA synthesis and proliferation of hLigI-deficient cells expressing either hLig51A or hLig51 was reduced compared with cells expressing wild-type hLigI, cellular senescence was only observed in the cells expressing hLigI51D. Notably, these cells had increased levels of spontaneous DNA damage and phosphorylated CHK2. In addition, although expression of hLigI51A complemented the sensitivity of hLigI-deficient cells to a poly (ADP-ribose polymerase (PARP) inhibitor, expression of hLig151D did not, presumably because these cells are more dependent upon PARP-dependent repair pathways to repair the damage resulting from the abnormal DNA replication. Finally, neither expression of hLigI51D nor hLigI51A fully complemented the sensitivity of hLigI-deficient cells to DNA alkylation. Thus, phosphorylation of serine 51 on hLigI plays a critical role in regulating the interaction between hLigI and RFC, which is required for efficient DNA replication and repair.     

Piezotolerance of the cytoskeletal structure in cultured deep-sea fish cells using DNA transfection and protein introduction techniques

We used DNA transfection and protein introduction techniques to investigate the pressure tolerance of cytoskeletal structures in pectoral fin cells derived from the deep-sea fish Simenchelys parasiticus (habitat depth, 366–2,630 m). The deep-sea fish cells have G418 resistance. The cell number increased until day 6 of cultivation and all cells had died by day 35 when cultured in 35-mm Petri dishes in medium containing G418. Enhanced yellow fluorescent protein-tagged human β-actin (EYFP-actin) was stably expressed by 1 in 100,000 deep-sea fish cells. Because almost none of the EYFP-actin was incorporated into actin filaments of the cells, we replaced the relatively large EYFP tag with a chemical fluorescent compound and succeeded in incorporating fluorescently labeled rabbit actins into the deep-sea fish actin filaments. Most of the filament structure in the cells with rabbit actin inserted underwent depolymerization when subjected to pressure of 100 MPa for 20 min, in contrast to control cells. There were no differences in the tubulin filament structure between control cells and deep-sea fish cells with fluorescein-labeled bovine tubulin inserted after the application of pressure ranging from 40 to 100 MPa for 20 min.     

Non-endocytic penetration of core histones into petunia protoplasts and cultured cells: a novel mechanism for the introduction of macromolecules into plant cells

The results of the present work demonstrate that core histones are able to penetrate the plasma membrane of plant cells. Confocal microscopy has revealed that incubation of petunia protoplasts with fluorescently labeled core histones resulted in cell penetration and nuclear import of the externally added histones. Intracellular accumulation was also confirmed by an ELISA-based quantitative method using biotin-labeled histones. Penetration into petunia protoplasts and cultured cells was found to be non-saturable, occurred at room temperature and at 4 °C and was not inhibited by Nocodazole. Furthermore, penetration of the biotinylated histone was neither blocked by the addition of an excess of free biotin molecules, nor by non-biotinylated histone molecules. All these results clearly indicate that the observed uptake is due to direct translocation through the cell plasma membrane and does not occur via endocytosis. Our results also show that the histones H2A and H4 were able to mediate penetration of covalently attached BSA molecules demonstrating the potential of the histones as carriers for the delivery of macromolecules into plant cells. To the best of our knowledge, the findings of the present paper demonstrate, for the first time, the activity of cell penetrating proteins (CPPs) in plant cells.     

Characteristics of enzymatic DNA methylation in cultured cells of human and hamster origin,and the effect of DNA replication inhibition

In mammalian cells, inhibitors of DNA replication have been shown to induce chromosomal aberrations, cell death and changes in gene control. Inhibition of DNA synthesis has been reported to induce hypermethylation of mammalian DNA (enzymatic postsynthetic formation of 5-methylcytosine). These 5-methylcytosines in mammalian DNA have variously been suggested to be important in gene control, DNA repair, and control of DNA replication. In establishing the normal characteristics of enzymatic DNA methylation, we have demonstrated that, in asynchronously growing cells of both human and hamster origin, some cytosine methylation is delayed for several hours after strand synthesis and that this delayed methylation is completed before the DNA strand acts as a template for DNA replication in the next S-phase. Further, in testing whether the deleterious effects on mammalian cells of DNA synthesis inhibitors might be mediated via changes in enzymatic DNA methylation, we have found, contrary to some previous findings, no evidence for any change in the level of DNA methylation in DNA strands synthesized during 6 h of treatment of cells of human origin with high concentrations of four different inhibitors of DNA replication or during the 4 h following the 6 h treatment. Almost totally blocking DNA replication had no effect on the small amount of delayed methylation of DNA strands not involved in semi-conservative replication during the time of the experiment. This lack of effect on DNA methylation was obtained when the labelling medium contained normal, undialysed serum. In contrast, if dialysed serum was used in the labelling medium in order to maximize l-[Me-³H]methionine utilization, highly variable, totally irreproducible patterns of apparent DNA hypermethylation were obtained.