Mycoplasma nucleases able to induce internucleosomal DNA degradation in cultured cells possess many characteristics of eukaryotic apoptotic nucleases

It was previously shown (Paddenberg et al (1996) Eur J Cell Biol 69, 105 - 119) that cells of established lines like NIH3T3 fibroblasts and the human pancreatic adenocarcinoma PaTu 8902 line only degrade their chromatin at internucleosomal sites after an apoptotic stimulus when infected with Mycoplasma hyorhinis. In order to distinguish mycoplasma nucleases (Mr 47 - 54 kDa) from already described eukaryotic apoptotic enzymes, the mycoplasma nucleases were partially purified from serum-free culture supernatants and further characterized. Here we demonstrate directly that the enriched mycoplasma nucleases were able to fragment the DNA of nuclease-negative substrate nuclei at internucleosomal sites. The DNA degradation was accompanied by morphological changes typical of apoptosis like chromatin condensation and margination followed by shrinkage of the nuclei. The biochemical characterization revealed that the mycoplasma nucleases had a neutral to weakly basic pH-optimum. They required both calcium and magnesium in the mM range for maximal activation and were inhibited by zinc chloride, EGTA and EDTA. In two dimensional zymograms they migrated as three spots with isoelectic points between 8.1 and 9.5. They were not inhibited by monomeric actin. Our data also demonstrate that nuclear extracts prepared from nuclei isolated from Mycoplasma hyorhinis infected cells contained the mycoplasma nuclease activities leading to their internucleosomal DNA-degradation after incubation in the presence of calcium and magnesium.     

Search for apoptotic nucleases in yeast: role of Tat-D nuclease in apoptotic DNA degradation

DNA fragmentation/degradation is an important step for apoptosis. However, in unicellular organisms such as yeast, this process has rarely been investigated. In the current study, we revealed eight apoptotic nuclease candidates in Saccharyomyces cerevisiae, analogous to the Caenorhabditis elegans apoptotic nucleases. One of them is Tat-D. Sequence comparison indicates that Tat-D is conserved across kingdoms, implicating that it is evolutionarily and functionally indispensable. In order to better understand the biochemical and biological functions of Tat-D, we have overexpressed, purified, and characterized the S. cerevisiae Tat-D (scTat-D). Our biochemical assays revealed that scTat-D is an endo-/exonuclease. It incises the double-stranded DNA without obvious specificity via its endonuclease activity and excises the DNA from the 3'- to 5'-end by its exonuclease activity. The enzyme activities are metal-dependent with Mg(2+) as an optimal metal ion and an optimal pH around 5. We have also identified three amino acid residues, His(185), Asp(325), and Glu(327), important for its catalysis. In addition, our study demonstrated that knock-out of TAT-D in S. cerevisiae increases the TUNEL-positive cells and cell survival in response to hydrogen hyperoxide treatment, whereas overexpression of Tat-D facilitates cell death. These results suggest a role of Tat-D in yeast apoptosis.     

Specific cleavage of chromatin by restriction nucleases.

Digestion of mouse and rat liver nuclei with a restriction nuclease from Bacillus subtilis (Bsu) is examined in continuation of previous work from this laboratory (Pfeiffer et al., 1975, Nature 258, 450). The finding of more than 95% C in the 5'-termini of the DNA fragments generated during digestion with Bsu shows that the participation of endogenous nucleases in Bsu digestion is extremely small. The restriction nuclease Hae III, an isoschizomer of Bsu, yields identical degradation patterns. The patterns conform to what one expects from statistical calculations based on a nucleosome structure of chromatin with a region preferentially accessible to the nuclease of 40-50 nucleotide pairs per nucleosome. Integrity of the histones is maintained during digestion with restriction nucleases. Digestion of mouse liver nuclei with EcoRII shows that most if not all of the satellite DNA is organized in a nucleosome structure. Also in rat liver, much of the repetitive DNA appears to be present in nucleosomes.     

Cations and the accessibility of chromatin to nucleases.

When rat liver nuclei prepared with polyamines as stabilising cations are digested with DNAase II, release of both inactive chromatin and Mg-soluble, active chromatin is greatly reduced, in comparison to digestion of liver nuclei prepared with Mg2+ as stabilising cation. Chromatin release from polyamine stabilised nuclei is also inhibited relative to Mg-stabilised nuclei following digestion with micrococcal nuclease under two very different cation conditions. Nuclei prepared with polyamines and monovalent ions as stabilising cations exhibit properties intermediate between these two extremes with both nucleases. These effects are due to residual binding of polyamines to chromatin, which is thus maintained in a condensed state, inaccessible to nucleases. Since polyamine binding is not easily reversed, concentrations of polyamines and other cations must be rigidly controlled in experiments on chromatin structure if artefacts are to be avoided. The significance of these findings to the nature and properties of active chromatin within the intact nucleus is considered.     

Stability of DNA-protein interactions in chromatin fractions with different sensitivity to nucleases

It was revealed by means of nucleoprotein-celite-chromatography that DNA-protein interactions in the chromatin fraction sensitive to micrococcal nuclease and DNase II are weaker that in the resistant one. The micrococcal nuclease destroys the DNA-matrix bond resistant to salt-urea, while DNase II does not change the DNA-matrix integrity. Tightness of the DNA-protein interactions is weakened by the increasing chromatin fragmentation, but does not depend on the size of chromatin particles.     

Dinucleosome as a product of initial chromatin cleavage by endogenous nucleases

The ability of nucleic endonucleases to recognize dinucleosomal level of chromatin structure was studied. Rat liver chromatin endonucleases were shown to be capable of DNA cleavage at dinucleosome linkers. The cleavage was observed mainly at initial stages of chromatin autohydrolysis, i.e. up to 10-20th min of incubation in the medium containing 5 mmol of magnesium chloride and 2 mmol of calcium chloride. Thus, mononucleosomal DNA in dinucleosomes and other even chromatin subunits was larger and more homogeneous than in odd subunits. The cleavage of autodigested chromatin by bovine spleen and snake venom exonucleases and by nuclease S1 has shown that dinucleosomal structure is independent of differences in the length of internal and external dinucleosome linkers. The initial endonucleolysis appears to be characterized by different accessibility of the linkers for chromatin nucleases.     

Degradation of chromatin in apoptotic cells

We present here a model for the degradation of chromatin in cells undergoing apoptosis. This model rationalises all aspects of the fragmentation process that have been described to date, explaining not only the patterns of degradation seen within individual cells, but also the variability in extent of degradation seen in different cells. Although DNA fragmentation in apoptosis was initially considered to be solely internucleosomal, it is now apparent that the process is much more complex and most, if not all, cells also produce much larger DNA fragments. However, in the same way that internucleosomal DNA fragmentation is a reflection of chromatin structure, the generation of these larger fragments is a reflection of chromatin structure, too. By comparing the ionic requirements for the complete pattern of chromatin degradation in nuclei with those required for apoptosis, it is apparent that the whole process may be catalysed by two pools of Mg-activated\Ca-modulated DNase I-like enzyme activities.     

In vitro assay of extracellular matrix elastin degradation

This report describes a method for determining specifically and sensitively the degradation of the elastin component within complicated extracellular matrices in vitro. Extracellular matrices rich in elastin were metabolically labeled with [3H]lysine during 3 week cultures of smooth muscle cells under ascorbate-free conditions in vitro. Elastin was quantitated on the basis of labeled desmosine/isodesmosine in the matrices as determined by a cation-exchange HPLC program utilizing a Beckman 6300 amino acid analyzer. The net loss of desmosine/isodesmosine during co-culture of human macrophages with the matrices was then used to assay cellular elastin degradation. This method allows for the production of reproducibly labeled matrices and compares favorably with previously described techniques of elastin degradation by live cells in vitro.     

In vitro cytotoxicity assay to evaluate the toxicity of an electrophilic reactive metabolite using glutathione-depleted rat primary cultured hepatocytes

Glutathione plays an important role as not only a scavenger of reactive oxygen species but also in the conjugation or detoxification of electrophilic reactive metabolites, which has been thought to be one of the causes for idiosyncratic drug toxicity (IDT). Therefore, toxic responses to the reactive metabolites have been expected to be expressed more strongly in a glutathione-depleted condition. In the present study, we attempted to establish an in vitro cytotoxicity assay method to evaluate the toxicity of the reactive metabolite using rat primary cultured hepatocytes with cellular glutathione depletion by l-buthionine-S,R-sulfoximine. Also, we investigated whether the IDT risk is predictable by comparing the cytotoxic sensitivity between glutathione-depleted hepatocytes and untreated hepatocytes. Consequently, 10 drugs of 42 approved drugs, which were classified into 4 IDT categories (Withdrawn, Black box warning, Warning, and Safe), demonstrated higher cytotoxic sensitivity in the glutathione-depleted hepatocytes. Furthermore, a correlation was observed between the incidence of drugs with higher cytotoxic sensitivity in the glutathione-depleted hepatocytes and the IDT risk. The incidence was 50% in the Withdrawn category, 38% in the Black box warning category, 22% in the Warning category, and 8% in the Safe category. These results suggest that the IDT risk of some drugs may be predicted by comparing the cytotoxic sensitivity between them. Additionally, this method may be useful as a screening in the early stage of drug development where leads/candidates are optimized.     

In vitro assay for the quantitative measurement of apoptotic lymphocytes phagocytosis by peripheral blood monocytes

Currently used assays for the quantification of apoptotic cells uptake by phagocytes have several methodological problems. Our assay overcomes some of these problems. As a source of apoptotic cells we used peripheral blood lymphocytes obtained from the patients with chronic lymphoblast leukaemia. Apoptosis was induced by incubating cells with cycloheximide for up to 24 h. The assay was performed in suspension of peripheral blood mononuclear cells. For the visualisation of the phagocytes and phagocyted cells and discrimination of phagocyted from bound apoptotic cells we used Acridine orange/Ethidium bromide double staining. Here we offer a simple test which enables reliable measurement and it can show the difference of phagocytic potential between different individuals.     

Revealing off-target cleavage specificities of zinc-finger nucleases by in vitro selection

Engineered zinc-finger nucleases (ZFNs) are promising tools for genome manipulation, and determining off-target cleavage sites of these enzymes is of great interest. We developed an in vitro selection method that interrogates 10(11) DNA sequences for cleavage by active, dimeric ZFNs. The method revealed hundreds of thousands of DNA sequences, some present in the human genome, that can be cleaved in vitro by two ZFNs: CCR5-224 and VF2468, which target the endogenous human CCR5 and VEGFA genes, respectively. Analysis of identified sites in one cultured human cell line revealed CCR5-224-induced changes at nine off-target loci, though this remains to be tested in other relevant cell types. Similarly, we observed 31 off-target sites cleaved by VF2468 in cultured human cells. Our findings establish an energy compensation model of ZFN specificity in which excess binding energy contributes to off-target ZFN cleavage and suggest strategies for the improvement of future ZFN design.     

Restoration of the primer activity of gamma-irradiated DNA by nucleases from rat liver chromatin

gamma-Irradiation of DNA results in a several-fold decrease of its primer activity measured as one substrate synthesis catalyzed by DNA polymerase beta. However, the combined treatment of injured DNA with 3'----5' exonuclease and endonuclease I from rat liver chromatin almost normalizes primer activity of DNA. Therefore the above-mentioned nucleases are capable of excising the gamma-injured nucleotides from 3'-OH ends of DNA.     

Utilization and degradation of an ester-based synthetic lubricant by Acinetobacter lwoffi

An oil-degrading bacterium, Acinetobacter lwoffi, isolated by elective culture from the Medway estuary, utilized an ester-based synthetic lubricating oil EMKARATE DE 155 as sole carbon and energy source. Analysis of culture supernatants by gas chromatography showed the accumulation of a nondegradable metabolite 1,1,1 Tris (hydroxymethyl) propane in addition to two metabolizable fatty acids, octanoic and decanoic acids as products of the synthetic oil degradation. Esterase activities were subsequently demonstrated in oil and acetate-grown cells. The synthetic oil therefore appears to be partially biodegradable in the environment.     

Utilization and degradation of an ester-based synthetic lubricant by Acinetobacter lwoffi

An oil-degrading bacterium, Acinetobacter lwoffi, isolated by elective culture from the Medway estuary, utilized an ester-based synthetic lubricating oil EMKARATE DE 155 as sole carbon and energy source. Analysis of culture supernatants by gas chromatography showed the accumulation of a nondegradable metabolite 1,1,1 Tris (hydroxymethyl) propane in addition to two metabolizable fatty acids, octanoic and decanoic acids as products of the synthetic oil degradation. Esterase activities were subsequently demonstrated in oil and acetate-grown cells. The synthetic oil therefore appears to be partially biodegradable in the environment.     

An in vitro assay for the selective endoplasmic reticulum associated degradation of an unglycosylated secreted protein

The endoplasmic reticulum (ER) represents the first compartment into which nascent secreted proteins traffic, and not coincidentally the ER lumen houses a high concentration of factors that facilitate protein folding, such as molecular chaperones. To off-set the potentially lethal consequences of mis-folded secreted protein accumulation, aberrant proteins may be selected for degradation via a process known as ER associated degradation (ERAD). After their selection ERAD substrates are retro-translocated back to the cytoplasm and then degraded by the 26S proteasome. Key features of the selection, retro-translocation, and degradation steps that constitute the ERAD pathway were elucidated through the development of an in vitro ERAD assay. In this assay the fates of two yeast proteins can be distinguished after their translocation, or import into ER-derived microsomes. Whereas a wild type, glycosylated protein ("Gp(alpha)F") is stable, a non-glycosylated version of the same protein ("p(alpha)F") is rapidly degraded when microsomes containing radiolabeled forms of these substrates are incubated in cytosol and ATP. The purpose of this chapter is first to discuss the experimental findings from the use of the in vitro assay, and then to describe the assay in detail. Finally, future potential uses of the in vitro system are illustrated.     

Deriving fractional rate of degradation of logistic-exponential (LE) model to evaluate early in vitro fermentation

Water-soluble components of feedstuffs are mainly utilized during the early phase of microbial fermentation, which could be deemed an important determinant of gas production behavior in vitro. Many studies proposed that the fractional rate of degradation (FRD) estimated by fitting gas production curves to mathematical models might be used to characterize the early incubation for in vitro systems. In this study, the mathematical concept of FRD was developed on the basis of the Logistic-Exponential (LE) model, with initial gas volume being zero (LE₀). The FRD of the LE₀ model exhibits a continuous increase from initial (FRD₀) toward final asymptotic value (FRD_F) with longer incubation time. The relationships between the FRD and gas production at incubation times 2, 4, 6, 8, 12 and 24 h were compared for four models, in addition to LE₀, Generalization of the Mitscherlich (GM), c^th order Michaelis–Menten (MM) and Exponential with a discrete LAG (EXP_LAG). A total of 94 in vitro gas curves from four subsets with a wide range of feedstuffs from different laboratories and incubation periods were used for model testing. Results indicated that compared with the GM, MM and EXP_LAG models, the FRD of LE₀ model consistently had stronger correlations with gas production across the four subsets, especially at incubation times 2, 4, 6, 8 and 12 h. Thus, the LE₀ model was deemed to provide a better representation of the early fermentation rates. Furthermore, the FRD₀ also exhibited strong correlations (P < 0.05) with gas production at early incubation times 2, 4, 6 and 8 h across all four subsets. In summary, the FRD of LE₀ model provides an alternative to quantify the rate of early stage incubation, and its initial value could be an important starting parameter of rate.     

Identification of apoptotic cells by formamide-induced dna denaturation in condensed chromatin.

In this article we describe a novel effect of formamide on DNA of apoptotic nuclei and present a method for specific detection of apoptotic cells based on this effect. Our observations show that formamide induces DNA denaturation in apoptotic nuclei but has no such effect on DNA of non-apoptotic cells. Formamide-induced DNA denaturation combined with detection of denatured DNA with a monoclonal antibody (MAb) against single-stranded DNA made it possible to specifically identify the apoptotic cells. This procedure produced intense staining of the condensed chromatin in the apoptotic nuclei. In contrast, necrotic cells from cultures treated with sodium azide, saponin, or hyperthermia did not bind this antibody, demonstrating the specificity of the formamide-MAb assay for the apoptotic cells. However, TUNEL stained 90-100% of necrotic cells in all three models of necrosis. Because the MAb did not stain cells with single- or double-stranded DNA breaks in the absence of apoptosis, we conclude that staining of the apoptotic nuclei is not influenced by DNA breaks and is induced by specific changes in condensed chromatin, such as damage to the DNA-histone interactions. Importantly, the formamide-MAb technique identified apoptotic cells in frozen sections and in histological sections of formalin-fixed, paraffin-embedded tissues.