Rapid "open-source" engineering of customized zinc-finger nucleases for highly efficient gene modification

Custom-made zinc-finger nucleases (ZFNs) can induce targeted genome modifications with high efficiency in cell types including Drosophila, C. elegans, plants, and humans. A bottleneck in the application of ZFN technology has been the generation of highly specific engineered zinc-finger arrays. Here we describe OPEN (Oligomerized Pool ENgineering), a rapid, publicly available strategy for constructing multifinger arrays, which we show is more effective than the previously published modular assembly method. We used OPEN to construct 37 highly active ZFN pairs which induced targeted alterations with high efficiencies (1%-50%) at 11 different target sites located within three endogenous human genes (VEGF-A, HoxB13, and CFTR), an endogenous plant gene (tobacco SuRA), and a chromosomally integrated EGFP reporter gene. In summary, OPEN provides an "open-source" method for rapidly engineering highly active zinc-finger arrays, thereby enabling broader practice, development, and application of ZFN technology for biological research and gene therapy.

Antitumor and biological effects of black pine (pinus nigra) pollen nuclease

The antitumor effect of black pine (Pinus nigra) pollen nuclease (PN) tested in vitro was negligible in comparison with bovine seminal ribonuclease (BS-RNase). However, in the experiments in vivo a significant decrease of the human melanoma tumor size was observed in the mice treated with this nuclease and also with the animal RNases and DNase I. In nude mice injected intratumoraly with PN (10 microg/dose) the tumor size decreased from 100% in the control mice to 46% in treated mice whereas in counterparts treated with BS-RNase and DNase I the tumor growth was reduced a little more, however after ten times higher doses (100 and 80 microg per dose). Certain aspermatogenic and embryotoxic activity as an expression of side effects of PN and comparative enzymes also appeared, but it was lower compared to the effect of bovine seminal ribonuclease. Immunogenicity of PN was significantly weaker in comparison with BS-RNase. The antibodies against black pine nuclease produced in the injected mice did not inactivate the biological effects of this plant nuclease in vivo. In conclusion PN nuclease proved in vivo higher antitumor activity against human melanoma tumors growing in athymic mice in comparison with animal bovine seminal ribonuclease and DNase I.

DNA Binding and Degradation by the HNH Protein ColE7

The bacterial toxin ColE7 bears an HNH motif which has been identified in hundreds of prokaryotic and eukaryotic endonucleases, involved in DNA homing, restriction, repair, or chromosome degradation. The crystal structure of the nuclease domain of ColE7 in complex with a duplex DNA has been determined at 2.5 A resolution. The HNH motif is bound at the minor groove primarily to DNA phosphate groups at and beyond the 3' side of the scissile phosphate, with little interaction with ribose groups and bases. This result provides a structural basis for sugar- and sequence-independent DNA recognition and the inhibition mechanism by inhibitor Im7, which blocks the substrate binding site but not the active site. Structural comparison shows that two families of endonucleases bind and bend DNA in a similar way to that of the HNH ColE7, indicating that endonucleases containing a "betabetaalpha-metal" fold of active site possess a universal mode for protein-DNA interactions.

Role of Mycoplasma penetrans endonuclease P40 as a potential pathogenic determinant

Recently, we reported the purification to homogeneity and characterization of Ca(2+)- and Mg(2+)-dependent endonuclease P40 produced by Mycoplasma penetrans (M. Bendjennat, A. Blanchard, M. Loutfi, L. Montagnier, and E. Bahraoui, J. Bacteriol. 179; 2210-2220, 1997), a mycoplasma which was isolated for the first time from the urine of human immunodeficiency virus-infected patients. To evaluate how this nuclease could interact with host cells, we tested its effect on CEM and Molt-4 lymphocytic cell lines and on peripheral blood mononuclear cells. We observed that 10(-7) to 10(-9) M P40 is able to mediate a cytotoxic effect. We found that 100% of cells were killed after 24 h of incubation with 10(-7) M P40 while only 40% cytotoxicity was obtained after 72 h of incubation with 10(-9) M P40. Phase-contrast microscopy observations of P40-treated cells revealed morphological changes, including pronounced blebbing of the plasma membrane and cytoplasmic shrinkage characteristic of programmed cell death, which is in agreement with the internucleosomal fragmentation of P40-treated cell DNA as shown by agarose gel electrophoresis. We showed that (125)I-radiolabeled or fluorescein isothiocyanate-labeled P40 was able to bind specifically in a dose-dependent manner to the cell membrane of CEM cells, which suggested that the cytotoxicity of P40 endonuclease was mediated by its interaction with the cell surface receptor(s). The concentration of unlabeled P40 required to inhibit by 50% the formation of (125)I-P40-CEM complexes was about 3 x 10(-9) M, indicating a high-affinity interaction. Both P40 interaction and cytotoxicity are Ca(2+) dependent. Our results suggest that the cytotoxicity of M. penetrans observed in vitro is mediated at least partially by secreted P40, which, after interaction with host cells, can induce an apoptosis-like death. These results strongly suggest a major role of mycoplasmal nucleases as potential pathogenic determinants.

Identification of residues in the putative TolA box which are essential for the toxicity of the endonuclease toxin colicin E9

E colicins are plasmid-coded, protein antibiotics which bind to the BtuB outer membrane receptor of Escherichia coli cells and are then translocated either to the outer surface of the cytoplasmic membrane in the case of the pore-forming colicin E1, or to the cytoplasm in the case of the enzymic colicins E2-E9. Translocation has been proposed to be dependent on a putative TolA box; a pentapeptide (DGSGW) located in the N-terminal 39 residues of several Tol-dependent colicins. In this study, site-directed mutagenesis was used to change each of the residues of the putative TolA box of colicin E9 to alanines. In the case of the two glycine residues, the resulting mutant proteins were indistinguishable from the native colicin E9 protein in a biological assay; whereas the other three residues when mutated to alanines resulted in a complete loss of biological activity. Mutagenesis of two serine residues flanking the putative TolA box, Ser34 and Ser40, to alanines did not abolish the biological activity of the mutant colicin E9, although the zones of growth inhibition were hazy and slow to form. The size of the zone of inhibition was significantly smaller than the control in the case of the Ser40Ala mutant. The ColE9/Im9 complex was isolated from the three biologically inactive TolA box alanine mutants. In competition assays all three mutant protein complexes were capable of protecting sensitive E. coli cells against killing by the native ColE9/Im9 complex. On removal of the Im9 protein from the three mutant ColE9/Im9 complexes, all three mutant colicins exhibited DNase activity. These results confirm the importance of the putative TolA box in the biological activity of colicin E9, and suggest that the TolA box has a role in the translocation of colicin E9.

Ultrasound permeabilizes CHO cells for the endonucleases AluI and benzon nuclease

Ultrasound permeabilizes Chinese hamster ovary (CHO) cells for the endonucleases AluI and benzon nuclease which leads to the induction of chromosomal aberrations by these enzymes. A few aberrant cells were observed when trypsinized cells or adherent cells were exposed to the enzymes in the absence of ultrasound. Our data show that sonication can be used to introduce endonucleases into CHO cells. We further demonstrate that few cells can internalize endonucleases without previous permeabilization.

Induction of chromosomal aberrations with benzon nuclease in Chinese hamster ovary (CHO) cells

Benzon nuclease, an endonuclease originating from Serratia marcescens, was tested for its chromosome breaking activity in Chinese hamster ovary cells. Using a permeabilizing method with hypertonic glycerol, benzon nuclease induced chromosomal aberrations in an S-phase independent manner. The frequencies of polycentric chromosomes were correlated with the dose of the enzyme and the intercellular distribution of aberrations was overdispersed.