Restriction Endonuclease BspD6II,a New Thermophilic Isoschizomer of Eco57I

Russian Journal of Bioorganic Chemistry - From the Bacillus species D6 strain, the restriction endonuclease BspD6II has been isolated and characterized. It recognizes the asymmetric region...     

Nicking endonucleases

Nicking endonucleases are a new type of enzymes. Like restriction endonucleases, they recognize short specific DNA sequence and cleave DNA at a fixed position relatively to the recognition sequence. However, unlike restriction endonucleases, nicking endonucleases cleave only one predetermined DNA strand. Until recently, nicking endonucleases were suggested to be naturally mutated restriction endonucleases which had lost their ability to dimerize and as a result the ability to cleave the second strand. We have shown that nicking endonucleases are one of the subunits of heterodimeric restriction endonucleases. Mechanisms used by various restriction endonucleases for double-stranded cleavage, designing of artificial nicking endonucleases on the basis of restriction endonucleases, and application of nicking endonucleases in molecular biology are reviewed.     

Association between intracellular proteinase activities and the content of locomotor proteins in tissues of primary tumors and metastases of ovarian cancer

The capability for active movement in an extracellular matrix, wherein remodeling of the cytoskeleton by actin-binding proteins plays a significant role, may influence the metastatic potential of tumor cells. We studied the expression of actin-binding proteins and β-catenin in connection with proteasome and calpain functions in tissues of primary tumors and metastases of ovarian cancer. The chymotrypsin-like proteasome activity and calpain activity were shown to be significantly higher in ovarian cancer than in normal tissues. Furthermore, the activity of the proteasome and calpain were significantly higher in the peritoneal metastases in comparison with primary tumors. Correlation analysis showed the presence of a positive correlation between the activity of calpain and chymotrypsin-like proteasome activity (r = 0.82; p = 0.0005) in primary tumor tissue, whereas no such correlation was revealed in metastases. Contents of p45 Ser β-catenin and the actin-severing protein gelsolin were decreased in metastases relative to primary tumors. The level of the cofilin, functionally similar to gelsolin, was significantly higher in metastases compared to primary ovarian tumor tissue. In ovarian cancer, significant reduction in the number of an actin-monomer binder protein thymosin-β4 was observed in primary tumors and metastases as compared to normal tissues, but no significant differences between primary tumors and metastases were observed. In tissues of primary tumors, negative correlations were observed between the chymotrypsin-like activity of proteasomes and the amounts of p45 Ser β-catenin and protein Arp3, a member of the Arp2/3 complex. In metastasis, negative correlation was revealed between the activity of calpain and the content of Arp3, cofilin, and thymosin. The data obtained suggest that the mechanisms of proteolytic regulation of locomotor proteins in primary tumors and metastases in ovarian cancer are different.     

Investigation of site-specific DNA binding with nicking endonuclease Nt.BspD6I at single molecule level by atomic force microscopy

Nicking endonuclease Nt.BspD6I is a heterodimeric restriction endonuclease, one subunit of which exhibits specific nicking activity. It gets bound to double-stranded DNA and makes a break (nick) in one chain at a distance of 4 nucleotides from the binding site. In this work, for visualization of the specific binding and protein landing site, atomic force microscopy was used. In five minutes after incubation of DNA solution with nicking endonuclease, DNA molecules with associated proteins which located at the expected binding site and “shared” the DNA strand into two segments (approximately, 1/3 and 2/3 of length) were observed in the images. In addition, near the binding site the DNA molecule had a height corresponding to a single-stranded DNA molecule, which was in good agreement with single-stranded cleavage by nickase in the course of complex formation.     

The Role of Cysteine Residues in the Interaction of Nicking Endonuclease BspD6I with DNA

Molecular Biology - Nicking endonucleases (NEs) are a small, poorly studied family of restriction endonucleases. The enzymes recognize a target sequence in DNA, but catalyze the hydrolysis of only...     

Isolation and characterization of exosomes from blood plasma of breast cancer and colorectal cancer patients

A simple approach for isolation of exosomes from blood plasma samples has been proposed. Using this approach it is possible to obtain highly purified preparations of microvesicles no larger than 100 nm. The presence of different subpopulations of exosomes isolated by this method has been recognized in the blood plasma of healthy donors and cancer patients. Universal markers CD9, CD24, and CD81 are applicable for routine typing of exosomes isolated from blood plasma samples.     

Nickase and a protein encoded by an open reading frame downstream from the nickase BspD6I gene form a restriction endonuclease complex

We are the first to have isolated a protein (186 amino acid residues) encoded by the open reading frame adjacent to the end of the BspD6I nickase (N.BspD6I) gene. Cleavage of both DNA strands near the sequence recognized by nickase (5 -GAGTC/5 -GACTC) occurs when this protein is added to the reaction mixture containing N.BspD6I. The protein encoded by the open reading frame and the nickase are suggested to be subunits of heterodimeric restriction endonuclease R.BspD6I.     

Structural analysis of the heterodimeric type IIS restriction endonuclease R.BspD6I acting as a complex between a monomeric site-specific nickase and a catalytic subunit

The heterodimeric restriction endonuclease R.BspD6I from Bacillus species D6 recognizes a pseudosymmetric sequence and cuts both DNA strands outside the recognition sequence. The large subunit, Nt.BspD6I, acts as a type IIS site-specific monomeric nicking endonuclease. The isolated small subunit, ss.BspD6I, does not bind DNA and is not catalytically active. We solved the crystal structures of Nt.BspD6I and ss.BspD6I at high resolution. Nt.BspD6I consists of three domains, two of which exhibit structural similarity to the recognition and cleavage domains of FokI. ss.BspD6I has a fold similar to that of the cleavage domain of Nt.BspD6I, each containing a PD-(D/E)XK motif and a histidine as an additional putative catalytic residue. In contrast to the DNA-bound FokI structure, in which the cleavage domain is rotated away from the DNA, the crystal structure of Nt.BspD6I shows the recognition and cleavage domains in favorable orientations for interactions with DNA. Docking models of complexes of Nt.BspD6I and R.BspD6I with cognate DNA were constructed on the basis of structural similarity to individual domains of FokI, R.BpuJI and HindIII. A three-helix bundle forming an interdomain linker in Nt.BspD6I acts as a rigid spacer adjusting the orientations of the spatially separated domains to match the distance between the recognition and cleavage sites accurately.