Sth132I,a novel class-IIS restriction endonuclease of Streptococcus thermophilus ST132

The Sth132I restriction endonuclease (R.Sth132I) was detected in Streptococcus thermophilus ST132 and purified to near homogeneity by heparin Sepharose CL-6B affinity chromatography. Fragments from Sth132I digestion of plasmid DNA were subcloned into pUC19 in Escherichia coli DH5α and sequenced. Sequence analysis of inserts and their ligation junction sites revealed that Sth132I is a novel class-IIS restriction endonuclease, which recognizes the non-palindromic sequence5′-CCCG(N)₄-3′3′-GGGC(N)₈-5′.     

The relaxation of specificity of BanI restriction endonuclease from Bacillus aneurinolyticus IAM 1077

The restriction endonuclease BanI from Bacillus aneurinolyticus IAM 1077, which recognizes 5′-GGPyPuCC-3′ and cleaves between G and G within this sequence, has decreased substrate specificity at high nuclease concentrations. The relaxation of its specificity was enhanced during modified reactions: digestion of pBR322 DNA or lambda DNA in the presence of high glycerol and dimethyl-sulfoxide (DMSO) produced additional fragments in addition to the inherent fragments. Therefore, it is required to check the reaction conditions carefully for generation of inherent fragments.     

The oxidative nuclease activity of human cytochrome c with mutations in Ω-loop C/D

Natural and artificial nucleases have extensive applications in biotechnology and biomedicine. The exploration of protein with potential DNA cleavage activity also inspires the design of artificial nuclease and helps to understand the physiological process of DNA damage. In this study, we engineered four human cytochrome c (Cyt c) mutants (N52S, N52A, I81N, and I81D Cyt c), which showed enhanced DNA cleavage activity and degradation in comparison with WT Cyt c, especially under acidic conditions. The mechanism assays revealed that the superoxide (O₂^??) plays an important role in the nuclease reaction. The kinetic assays showed that the peroxidase activity of the I81D Cyt c mutant enhanced up to 9-fold at pH 5. This study suggests that the mutations of Ile81 and Asn52 in Ω-loop C/D are critical for the nuclease activity of Cyt c, which may have physiological significance in DNA damage and potential applications in biomedicine.     

A specific endonuclease from Brevibacterium albidum

A new restriction-like endonuclease, BalI, has been partially purified from Brevibacterium albidum. This enzyme cleaves bacteriophage λ DNA at least 18 times and adenovirus-2 DNA at least 16 times, but does not cleave simian virus 40 DNA. All sites cleaved by BalI are also cut by the specific endonuclease HaeIII from Haemophilus aegyptius. The recognition sequence of BalI is 5′-T-G-G ↓ C-C-A-3′ 3′-A-C-C ↓ G-G-T-5′ and the cleavage site is indicated by the arrows.     

A possible cause of heterogeneity of mammalian apurinic/apyrimidinic endonuclease

• 1.1. Mammalian major apurinic/apyrimidinic (AP) endonuclease, APEX nuclease (M_r 35.4 kDa) was purified from HeLa cells. A hybrid protein (M_r 36.4 kDa), which was expressed in BW2001 strain cells of E. coli, comprising human APEX nuclease headed by 10 additional amino acids was also purified.
• 2.2. The purified preparations were frequently associated with 31-, 33- and 35-kDa peptides having AP endonuclease activity.
• 3.3. The 33- and 35-kDa peptides were suggested to be formed from the hybrid protein or APEX nuclease during their purification processes by proteolytic cleavage with subtilisin-like protease. The 31-kDa peptide was thought to be produced by chemical cleavage of the aspartyl-prolyl bond of APEX nuclease.
• 4.4. The results support the notion that some of AP endonuclease heterogeneity based on the molecular weight difference are caused by proteolytic (and chemical) cleavage of a species of AP endonucleases during the extraction and purification.

     

Cloning of restriction and modification genes in E. coli: The HhaII system from Haemophilus haemolyticus

The genes for a Class II restriction-modification system (HhaII) from Haemophilus haemolyticus have been cloned in Escherichia coli. The vector used for cloning was plasmid pBR322 which confers resistance to tetracycline and ampicillin and contains a single endonuclease R·PstI site, (5′)C-T-G-C-A^↓-G (3′), in the ampicillin gene. The procedure developed by Bolivar et al. (1977) was used to form DNA recombinants. H. haemolyticus DNA was cleaved with PstI endonuclease and poly(dC) extensions were added to the 3′-OH termini using terminal deoxynucleotidyl transferase. Circular pBR322 DNA was cleaved to linear molecules with PstI endonuclease and poly(dG) extensions were added to the 3′-OH termini, thus regenating the PstI cleavage site sequence. Recombinant molecules, formed by annealing the two DNAs, were used to transfect a restriction and modification-deficient strain of E. coli (HB101 r^?m^?recA). Tetracycline-resistant clones were tested for acquisition of restriction phenotype (as measured by growth on plates seeded with phage λcI·O). A single phage-resistant clone was found. The recombinant plasmid, pDI10, isolated from this clone, had acquired 3 kilobases of additional DNA which could be excised with PstI endonuclease. In addition to the restriction function, cells carrying the plasmid expressed the HhaII modification function. Both activities have been partially purified by single-stranded DNA-agarose chromatography. The cloned HhaII restriction activity yields cleavage patterns identical to HinfI. A restriction map of the cloned DNA segment is presented.     

S1 nuclease of Aspergillus oryzae: characterization of the associated phosphomonoesterase activity

S₁ nuclease (EC 3.1.30.1) of Aspergillus oryzae was found to catalyze the hydrolysis of 2′- or 3′-phosphomonoester groups from several mono- and oligonucleotides. The specificity of the enzyme for mononucleotide substrates was determined by steady-state kinetic measurements at pH 4.5. The values of V were similar for all ribonucleoside 3′-phosphates tested, and they were 50–400 times greater than those for the corresponding deoxyribonucleotides or ribonucleoside 2′-phosphates. Purine nucleotides had lower apparent K_m values than pyrimidine nucleotides. Apparent K_m values of mononucleotides were also strongly dependent on the type of sugar and the positions of phosphoryl groups. Substrate specificity, as expressed by $\text{V}\text{K}{}_{\mathrm{m}}$, occurred in the following order: ribonucleoside 3′,5′-bisphosphate > ribonucleoside 3′-phosphate > deoxyribonucleoside 3′,5'-bisphosphate > deoxyribonucleoside 3′-phosphate ≈ ribonucleoside 2′-phosphate. S₁ nuclease also catalyzed the dephosphorylation of the dinucleotide ApAp at a high rate and the release of PP_i from adenosine 3′-diphosphate 5′-phosphate at a low rate. The phosphomonoesterase activity of the enzyme was competitively inhibited by single-stranded DNA and 5′-nucleotides. Apparent K_i values for adenosine compounds occurred in the order ATP < ADP < AMP ? adenosine. Tests of S₁ nuclease for phosphotransferase activity at pH 4.5 and 7.0 were negative.     

Introgression of <Emphasis Type="Italic">UfCyt c</Emphasis><Subscript>6</Subscript>, a thylakoid lumen protein from a green seaweed <Emphasis Type="Italic">Ulva fasciata</Emphasis> Delile enhanced photosynthesis and growth in tobacco

Cytochromes are important components of photosynthetic electron transport chain. Here we report on genetic transformation of Cytochrome c₆ (UfCyt c₆) gene from Ulva fasciata Delile in tobacco for enhanced photosynthesis and growth. UfCyt c₆ cDNA had an open reading frame of 330 bp encoding a polypeptide of 109 amino acids with a predicted molecular mass of 11.65 kDa and an isoelectric point of 5.21. UfCyt c₆ gene along with a tobacco petE transit peptide sequence under control of CaMV35S promoter was transformed in tobacco through Agrobacterium mediated genetic transformation. Transgenic tobacco grew normal and exhibited enhanced growth as compared to wild type (WT) and vector control (VC) tobacco. Transgenic tobacco had higher contents of photosynthetic pigments and better ratios of photosynthetic pigments. The tobacco expressing UfCyt c₆ gene exhibited higher photosynthetic rate and improved water use efficiency. Further activity of the water-splitting complex, photosystem II quantum yield, photochemical quenching, electron transfer rate, and photosynthetic yield were found comparatively higher in transgenic tobacco as compared to WT and VC tobacco. Alternatively basal quantum yield of non-photochemical processes in PSII and non-photochemical quenching were estimated lower in tobacco expressing UfCyt c₆ gene. As a result of improved photosynthetic performance the transgenic tobacco had higher contents of sugar and starch, and exhibited comparatively better growth. To the best of our knowledge this is the first report on expression of UfCyt c₆ gene from U. fasciata for improved photosynthesis and growth in tobacco.     

Generating Nucleosomal Ladders In Vivo by Releasing Endogenous Endonucleases in <Emphasis Type="Italic">Chlamydomonas reinhardtii</Emphasis>

Chromatin maps by enzymatic digestion using micrococcal nuclease (MNase) have served as popular substrates for molecular epigenetic studies. Such analyses have been limited to cell wall minus mutants of Chlamydomonas reinhardtii because of the complications in nucleus isolation due to cell wall removal. Here, we describe an endogenous endonuclease in Chlamydomonas that is specifically released from the cells upon abrasion with beads (glass or zirconia), in the presence of detergents. The resulting in vivo digests obtained from both cell wall containing cc124/cc125 and mutant strains (cc400) are typical of repetitive nucleosomal fragments (MNase-like ladders) ranging from mono- to poly-nucleosomes, indicating that the nuclease acts preferentially on inter-nucleosomal linker DNA. We demonstrate that the endonuclease activity is strictly dependent on divalent cations (Ca⁺²?>?Mg⁺²) and can be inhibited by both Cu⁺² and Zn⁺² (5 mM) or by divalent cation chelators like EDTA. Detailed standardization reveals that the nuclease is released only when the cells are treated with detergents, implying that it might be membrane bound or vesicular and intracellular in nature. This endonuclease seems to accumulate in late log-phase cultures and probably has a role in generation of apoptotic ladders in Chlamydomonas. Further activity-based in-gel DNase analyses of whole cell extracts, using denaturing SDS-PAGE, revealed a single major ~?30-kDa band upon renaturation. We further characterized this endonuclease by partial purification using ammonium sulfate precipitation. Activity-based analysis revealed partial enrichment in the 50% (NH₄)₂SO₄ peak fraction and also confirmed Ca dependence. Finally, adding back the released endonuclease from a detergent-treated supernatant of cc124 cells to intact cc400 cw ^? cells as substrate resulted in a typical ladder formation in the latter, confirming the intracellular release of the nuclease and its activity. In summary, by controlled release of calcium-dependent endogenous endonucleases (altering vortex and detergent conditions), we can generate dose-dependent nucleosomal ladders for epigenetic analyses in Chlamydomonas, as an alternate to MNase-derived substrates.     

Two sequence-specific endonucleases from Moraxella bovis

Two new sequence-specific endodeoxyribonucleases have been partially purified from Moraxella bovis. These restriction-like enzymes, MboI and MboII, each cleave bacteriophage lambda DNA and adenovirus-2 DNA at more than 50 sites. MboI recognizes the sequence 5′ ↓ G-A-T-C 3′ 3′ C-T-A-G ↑ 5′ and cleaves at the sites indicated by the arrows. A specific endonuclease, MosI, has also been purified from Moraxella osloenis and recognizes the same sequence as MboI.     

The origin of multiple polypeptides of molecular weight below 110 000 encoded by tobacco mosaic virus RNA in the messenger-dependent rabbit reticulocyte lysate

Multiple polypeptides encoded by tobacco mosaic virus (TMV) RNA in the messenger-dependent rabbit reticulocyte lysate are not attributable to contaminating 3′-coterminal RNA fragments, multiple leaky termination codons or endonuclease activity opening-up legitimate or spurious internal initiation sites. Quantitative analysis of polypeptides encoded over a range of added RNA concentrations from 0.09 μg·ml^?1 to 180 μg·ml^?1 compared wi preparation, or with RNA extracted from the alkali-stable fraction of TMV suggest that apart from four legitimate virus-coded products of apparent M_r approx. 165 000, 110 000, 30 000 and 17 500 all other polypeptides arise from the overlapping 5′-proximal cistrons either by (i) site-selective endonucleolytic cleavage, (ii) sense codon misreading, or (iii) specific regions of secondary structure on TMV RNA which impede ribosome translocation.     

Physical mapping and characterization of Chlamydomonas mitochondrial DNA molecules: Their unique ends,sequence homogeneity,and conservation

Sixteen site-specific endonucleases were used to characterize the mitochondrial (mt)-DNA of Chlamydomonas reinhardtii. Recognition sites for SmaI, XhoI, and BglII were absent in the mtDNA. mtDNA fragments appeared in stoichiometric proportions in every nuclease digest indicating that C. reinhardtii mtDNA consists of a homogenous population of molecules devoid of either inter- or intramolecular heterogeneity. Six DNA fragment maps were derived for those endonucleases that produced discrete and readily measurable DNA fragments. These maps, which exhibited marked internal consistency, also suggested that the linear mtDNA molecules possessed unique ends. This was subsequently confirmed by in vitro 5′-end labeling of mtDNA molecules prior to endonuclease digestion. These results indicate that (1) the linear mtDNA isolated under our experimental conditions possessed not only unique ends but also a nonpermuted gene sequence and (2) such mtDNA molecules were generated by a site-specific cleavage of the closed circular mtDNA molecules shown to exist in vivo. mtDNA sequence conservation in Chlamydomonas is quite striking. No difference in endonuclease cleavage pattern has yet been detected among a number of C. reinhardtii strains or between mating types.     

A new site-specific endonuclease from Streptomyces lavendulae (SlaI)

A new restriction-like endonuclease, SlaI, was found and partially purified from Streptomyces lavendulae ATCC8664. This endonuclease cleaved bacteriophage lambda DNA at only one site, and cytosine-substituted bacteriophage T4 DNA at 16 sites. The recognition sequence was determined by using SlaI fragments of cytosine-substituted bacteriophage T4 DNA. The hexanucleotide recognized by SlaI endonuclease was

$\text{5′-}\text{C}\text{?}\text{T}\text{-}\text{C}\text{-}\text{G}\text{-}\text{A}\text{-}\text{G}\text{-3′}$

$\text{3′-}\text{G}\text{-}\text{A}\text{-}\text{G}\text{-}\text{C}\text{-}\text{A}\text{-↑}\text{C}\text{-5′}$

with the sites of cleavage as indicated by the arrows. Therefore, SlaI endonuclease was an isochizomer of XhoI endonuclease.     

Characterization of DNA restriction and modification activities in Neisseria species

Type II restriction endonuclease activities detected in various Neisseria species were characterized for sequence specificity and precise site of cleavage. NsiCI isolated from N. sicca C351 cleaves the sequence 5′-GAT↓ATC-3′ (EcoRV isoschizomer); NmeCI from N. meningitidis C114 and NphI from N. pharyngis C245 cleave 5′-N↓GATCN-3′ (MboI isoschizomers); NgoPII and NgoPIII from N. gonorrhoeae P9-2 cleave at 5′-CC↓GCGG-3′ (SacII isoschizomer) and 5′-GG↓CC-3′ (HaeIII isoschizomer), respectively. Chromosomal DNA isolated from these strains and two other N. meningitidis strains (which lacked detectable endonuclease activities), was found to be refractive to cleavage by various restriction enzymes, implying the presence of methylase activities additional to those required for protection against the cellular endonucleases.     

Exo1 and Mre11 execute meiotic DSB end resection in the protist Tetrahymena

The resection of 5′-DNA ends at a double-strand break (DSB) is an essential step in recombinational repair, as it exposes 3′ single-stranded DNA (ssDNA) tails for interaction with a repair template. In mitosis, Exo1 and Sgs1 have a conserved function in the formation of long ssDNA tails, whereas this step in the processing of programmed meiotic DSBs is less well-characterized across model organisms. In budding yeast, which has been most intensely studied in this respect, Exo1 is a major meiotic nuclease. In addition, it exerts a nuclease-independent function later in meiosis in the conversion of DNA joint molecules into ZMM-dependent crossovers. In order to gain insight into the diverse meiotic roles of Exo1, we investigated the effect of Exo1 deletion in the ciliated protist Tetrahymena. We found that Exo1 together with Mre11, but without the help of Sgs1, promotes meiotic DSB end resection. Resection is completely eliminated only if both Mre11 and Exo1 are missing. This is consistent with the yeast model where Mre11 promotes resection in the 3′–5′ direction and Exo1 in the opposite 5′–3′ direction. However, while the endonuclease activity of Mre11 is essential to create an entry site for exonucleases and hence to start resection in budding yeast, Tetrahymena Exo1 is able to create single-stranded DNA in the absence of Mre11. Excluding a possible contribution of the Mre11 cofactor Sae2 (Com1) as an autonomous endonuclease, we conclude that there exists another unknown nuclease that initiates DSB processing in Tetrahymena. Consistent with the absence of the ZMM crossover pathway in Tetrahymena, crossover formation is independent of Exo1.     

Interferon, double-stranded RNA and RNA degradation. Fractionation of the endonucleaseINT system into two macromolecular components; role of a small molecule in nuclease activation

We reported earlier that a) the incubation of an extract from interferon-treated Ehrlich ascites tumor cells with double-straded RNA and ATP results in the activation of an endonuclease and b) after the activation the double-stranded RNA and ATP can be degraded without impairing the activity of the endonuclease. We report now the separation and partial purification of two macromolecular components (DE1_INT and DE2_INT) involved in the process. Upon incubation with double-stranded RNA and ATP component DE1_INT generates a heat-stable product of low molecular weight (designated as nuclease activator). On incubation with the nuclease activator a latent nuclease in component DE2_INT is activated.     

Structure analysis of three T7 late mRNA ribosome binding sites

The 5′-terminal regions of the three T7 late RNA species IIIb, IV and V have been characterized. These regions contain the protein synthesis initiation sites for the T7 genes 17, 9 and 10, respectively. Each of these is located between 60 and 90 nucleotides from the 5′ terminus of an in vitro synthesized RNA species. The sequence 5′ A-C-U-U-U-A-A-G-Pu-A-G-Pu, which is common to these ribosome binding regions, contains an impressive stretch of complementarity to the sequence 5′ A-C-C-U-C-C-U-U-A, at the 3′ terminus of 16 S ribosomal RNA. The nuclease mapping technique of Wurst et al. (1978) has been used to probe intramolecular structural interactions involving these initiation regions in the RNA. My results indicate that all three initiation codons, together with other portions of the ribosome binding regions are protected, under non-denaturing conditions, against the actions of both the single-strand-specific nuclease S₁ and RNAase T₁.