Essential role of the iron-sulfur cluster binding domain of the primase regulatory subunit Pri2 in DNA replication initiation

DNA primase catalyzes de novo synthesis of a short RNA primer that is further extended by replicative DNA polymerases during initiation of DNA replication. The eukaryotic primase is a heterodimeric enzyme comprising a catalytic subunit Pri1 and a regulatory subunit Pri2. Pri2 is responsible for facilitating optimal RNA primer synthesis by Pri1 and mediating interaction between Pri1 and DNA polymerase α for transition from RNA synthesis to DNA elongation. All eukaryotic Pri2 proteins contain a conserved C-terminal iron-sulfur (Fe-S) cluster-binding domain that is critical for primase catalytic activity in vitro. Here we show that mutations at conserved cysteine ligands for the Pri2 Fe-S cluster markedly decrease the protein stability, thereby causing S phase arrest at the restrictive temperature. Furthermore, Pri2 cysteine mutants are defective in loading of the entire DNA pol α-primase complex onto early replication origins resulting in defective initiation. Importantly, assembly of the Fe-S cluster in Pri2 is impaired not only by mutations at the conserved cysteine ligands but also by increased oxidative stress in the sod1Δ mutant lacking the Cu/Zn superoxide dismutase. Together these findings highlight the critical role of Pri2's Fe-S cluster domain in replication initiation in vivo and suggest a molecular basis for how DNA replication can be influenced by changes in cellular redox state.

New nsp8 isoform suggests mechanism for tuning viral RNA synthesis

During severe acute respiratory syndrome coronavirus (SARS-CoV) infection, the activity of the replication/transcription complexes (RTC) quickly peaks at 6 hours post infection (h.p.i) and then diminishes significantly in the late post-infection stages. This "down-up-down" regulation of RNA synthesis distinguishes different viral stages: primary translation, genome replication, and finally viron assembly. Regarding the nsp8 as the primase in RNA synthesis, we confirmed that the proteolysis product of the primase (nsp8) contains the globular domain (nsp8C), and indentified the resectioning site that is notably conserved in all the three groups of coronavirus. We subsequently crystallized the complex of SARS-CoV nsp8C and nsp7, and the 3-D structure of this domain revealed its capability to interfuse into the hexadecamer super-complex. This specific proteolysis may indicate one possible mechanism by which coronaviruses to switch from viral infection to genome replication and viral assembly stages.

[Evaluation of touchdown nested PCR to circumvent spurious priming and increase specificity during HIV and GBV-C gene amplification]

Primer-Template hybridization temperature is one of the important parameters in Nested PCR optimization. Unlike instant temperature for sequence amplification in routine PCR process, Touchdown PCR is a modified form of standard PCR that employs a range of annealing temperature. This study intended to develop a Touchdown Nested PCR in order to circumvent spurious priming and enhancing specify during gene amplification. This is an experimental study conducted at Tarbiat Modarres University of Tehran during 2008-2009. Study samples were collected from Digestive Diseases Research Centre at Shariati Hospital and HIV research center-Imam Khomeini Hospital. After extracting the nucleic acid, primer designing for HIV and GBV-C and c-DNA synthesis; Nested PCR was performed on negative and positive samples using standard and touchdown protocols. The intended band was observed in all positive samples. No band was observed in any human and viral negative control samples. After electrophoresis of PCR products, non specific band were seen in HIV and GBV-C samples during standard PCR. Using the touchdown protocol, undesirable bands were omitted or significantly decreased. In the present study, despite the formation of uncalled bands in standard reaction; using the touchdown method led to omission of non-specific bands without any significant effect on the final products. As for its simplicity, cost and time saving, it seems that using this method is a rational and economical way for fast optimization of PCR reactions

Investigation on mtDNA deletions and twinkle gene mutation (G1423C) in Iranian patients with chronic progressive external opthalmoplagia.

BACKGROUND: Chronic progressive external ophthalmoplagia (CPEO) is a phenotypic mitochondrial disorder that affects external ocular and skeletal muscles and is associated with a single or multiple mitochondrial DNA (mtDNA) deletions and also nuclear gene mutations. There are also some reports about the relationship between CPEO and the nuclear Twinkle gene which encodes a kind of mitochondrial protein called Twinkle. AIMS: To study the mtDNA deletions and Twinkle gene G1423C point mutation in Iranian patients with CPEO. MATERIALS AND METHODS: We collected 23 muscle samples from patients with CPEO, 9 women (mean age 34.3 years) and 14 men (36.7 years). Multiplex polymerase chain reaction (PCR) method was used to find the presence of single or multiple deletions in mtDNA. Single stranded conformational polymorphism (SSCP) and restriction fragment length polymorphism (PCR-RFLP) methods were carried out to investigate point mutation (G1423C) in the Twinkle gene in all DNA samples. RESULTS: Different sizes of mtDNA deletions were detected in 16 patients (69.6%). Each of the 5.5, 7, 7.5 and 9 kb deletions existed only in 1 patient. Common deletion (4977bp) and 8 kb deletion were detected in 5 and 3 patients respectively. Multiple deletions were also present in 4 patients. Out of 23 patients included in our study, two cases (8.7%) had Twinkle gene mutation (G1423C) and 5 patients (21.7%) did not show any deletions in mtDNA or the Twinkle gene mutation. CONCLUSION: Our study provides evidence that the investigation of mtDNA and Twinkle gene mutations in CPEO may help with early diagnosis and prevention of the disease. Patients who did not show deletions in the mtDNA or G1423C mutation in the Twinkle gene may have other mtDNA, Twinkle or nuclear gene mutations.

Apoptosis induced by DNA primase inhibitor 3,3'-diethyl-9-methylthia-carbocyanine iodide in human leukemia HL-60 cells / 药学学报

<p><b>AIM</b>To investigate apoptosis induced by 3,3'-diethyl-9-methylthia-carbocyanine iodide (DMTCCI), an inhibitor of DNA primase found in our previous study, and the mechanism of DMTCCI in human myelogenous leukemia HL-60 cells.</p><p><b>METHODS</b>HL-60 cells were cultured in RPMI-1640 medium and treated with different concentrations of DMTCCI. MTT assay was used to detect growth inhibition. Flow cytometry and DNA ladders were used to detect apoptosis. Western blotting was used to observe the expression of survivin, Bcl-xL, Bad, Bax, Bcl-2, caspase-9, caspase-3, caspase-6, PARP, DFF45 and lamin B protein. Caspase-3 activity was measured by ApoAlert Caspase-3 Assay Kit.</p><p><b>RESULTS</b>DMTCCI inhibited proliferation of human leukemia HL-60 cells with IC50 value of 0.24 micromol x L(-1). The results of flow cytometry and DNA ladders showed that DMTCCI could induce apoptosis of HL-60 cells. The expression levels of protein survivin and Bcl-xL were down-regulated, Bad and Bax were up-regulated, while Bcl-2 protein had no change in response to DMTCCI treatment in HL-60 cells. Treatment of HL-60 cells with DMTCCI induced the proteolytic cleavage of caspase-9, caspase-3, caspase-6, PARP, DFF45 and lamin B protein. Caspase-3 activity apparently increased at 3 h and reached a peak at 12 h after exposure to 1 micromol x L(-1) of DMTCCI in HL-60 cells.</p><p><b>CONCLUSION</b>DMTCCI inhibited proliferation and induced apoptosis of human leukemia HL-60 cells. Bcl-2 family proteins, survivin and caspases family proteins might play a role in the apoptosis process induced by DMTCCI.</p>

The Gene Expression Profile Using cDNA microarray after treatment Arsenic Compound (As2O3, As4O6) in SiHa Cell / 대한산부인과학회잡지

OBJECTIVE: To obtain information on the growth inhibition effect of arsenic compounds and gene expression profiles using cDNA microarray technique in SiHa cell lines. METHODS: We cultured 103 SiHa cell in 96 well plate and we investigated growth inhibition effects using MTT assay and also we performed gene expression profile experiment using 384 cDNA chip in SiHa cell after exposure of arsenics (As2O3, As4O6 - 1 (micro)M) for 48 hrs. RESULTS: Arsenics (As2O3, As4O6) inhibit the growth of SiHa cells (As2O3: 0.5, 1, 2, 3, 4, 5 (micro)M - 9.2, 56, 89, 93, 96, 96%, As4O6: 0.5, 1, 2, 3, 4, 5 (micro)M- 54, 84, 84, 85, 85, 87%) in 4 days culture. As2O3 and As4O6 induced apoptosis in SiHa cells. After exposure of As2O3, 47 genes were changed more than 2 times (eg, thymidylate synthetase, cyclin B1, CDC 20). In case of As4O6, 78 genes were changed more than 2 times (eg, CDC 20, cyclin B1, primase, proliferating cell nuclear antigen). CONCLUSION: we observed arsenic compound (As2O3, As4O6) inhibit the growth of SiHa cell. In gene expression profiling experiment, 78 genes was changed the expression level 2 times more than that of reference RNA after treatment of As4O6 and 47 genes after treatment of As2O3. Through these result, we thought more study need in functional genomics after arsenic treated cervical cancer cells.

Primase structure and function.

Primase is the ssDNA-dependent RNA polymerase that synthesizes RNA primers during DNA replication. In common with all DNA and RNA polymerases, primase has structural and functional features involved in polymer elongation. As RNA polymerase, it has structural and functional features for initiating chain synthesis. As a primase, it has structural and functional features for initiating chain synthesis on ssDNA. Using amino acid sequence analysis the structure of Escherichia coli primase responsible for binding zinc, at least three magnesium, and DnaB helicase has been identified. One of the magnesium binding motifs resembles the ¿active magnesium¿ motif found in all DNA and RNA polymerases. This motif can be considered to be involved in phosphodiester bond formation. The region with the putatuve zinc binding motif is the most highly conserved portion, including more than 25% of identical residues among bacterial primases. The function of the zinc finger may be to bind ssDNA in a sequence-specific manner. Primase has ¿RNAP¿ motif, a sequence found in all RNA polymerases which may be involved in chain initiation. Many of the observations concerning primer synthesis initiation in vivo have been reproduced by several of the in vitro assay systems. Important among these is that Okazaki fragments are initiated in vivo from d(CTG) most of the time. This trinucleotide initiation specificity has been shown to be an intrinsic property of pure primase in vitro. Using artificial ssDNA templates, primase has been shown to be the slowest and most error-prone polymerase yet studied. The rate-determining step is the first phosphodiester bond formed. Any protein which can influence either the dinucleotide synthesis rate or primase-ssDNA binding affinity will also play a key role in the regulation of primer synthesis initiation.

Characterization of DNA polymerase-alpha/primase complex from developing embryonic chicken brains.

DNA polymerase-alpha and primase activities present in a complex, have been isolated, partially purified, and characterized from embryonic chicken brain. DNA polymerase-alpha activity, characterized by its sensitivity to N-ethyl-maleimide, high sedimentation coefficient (11.3 S), and acidic isoelectric point (5-5.5) was found in all embryonic ages. Primase activity, the enzyme responsible for the initiation of DNA synthesis, co-sedimented with DNA polymerase-alpha activity on a continuous glycerol velocity gradient. A complex containing both DNA polymerase-alpha and primase activities was isolated by DE-23 cellulose column chromatography of cell-free extracts of different embryonic ages of chicken brain. In addition to the primase complexed with DNA polymerase-alpha, a free primase activity was isolated by DE-23 cellulose column chromatography of an ammonium sulfate (0-45%; w/v) precipitated fraction of embryonic chicken brain cell-free extract. DNA polymerase-alpha activity from developing chicken brains in the embryonic stage was purified by immuno-affinity column chromatography. Of all the single-stranded DNA templates tested, primase activity was found to be maximally active with poly dC. Primase activity was not inhibited by a high concentration of alpha-amanitin. The results obtained may provide insight into further understanding of regulation of chromosomal DNA replication in developing tissues.