Structure and function of DNA methyltransferases

In prokaryotes, the major role of DNA methylation is to protect host DNA against degradation by restriction enzymes. In eukaryotes, DNA methylation has been implicated in the control of several cellular processes, including differentiation, gene regulation, and embryonic development. Structural work on HhaI DNA methyltransferase demonstrates that the substrate nucleotide is completely flipped out of the helix during the modification reaction and has provided much insight into the enzymatic properties of S-adenosyl-L-methionine (SAM)-dependent DNA-modifying enzymes. Structural comparison of three enzymes, HhaI C5-cytosine methyltransferase, TaqI N6-adenine methyltransferase, and catechol O-methyltransferase, reveals a striking similarity in protein folding and indicates that many SAM-dependent methyltransferases have a common catalytic-domain structure. This feature permits the prediction of tertiary structure for other DNA, RNA, protein, and small-molecule methyltransferases from their amino acid sequences, including the eukaryotic CpG methyltransferases.

Structure-based sequence alignment of three AdoMet-dependent DNA methyltransferases

M.HhaI, M.TaqI and COMT are DNA methyltransferases (MTases) which catalyze the transfer of a methyl group from the cofactor AdoMet to C5 of cytosine, to N6 of adenine and to a hydroxyl group of catechol, respectively. The larger catalytic domains of the bilobal proteins, M.HhaI and M.TaqI, and the entire single domain of COMT have an alpha/beta structure containing a mixed central beta-sheet. These domains have very similar folding. By allowing appropriate 'insertions' or 'deletions' in the backbones of the three structures, it was possible to find more conserved motifs in M.TaqI and COMT. The similarity in protein folding and the equivalence of amino-acid sequences revealed by the structural alignment indicate that many AdoMet-dependent MTases may share a common catalytic domain structure.

Crystal structure of the PvuII restriction endonuclease

Crystal structures have now been determined for the R.PvuII restriction endonuclease as a protein-DNA complex [Cheng et al., EMBO J. 13 (1994) 3927-3935; this report] and in apo-form [Athanasiadis et al., Nature Struc. Biol. 1 (1994) 469-475; our unpublished result]. The structures indicate how the interaction with DNA might proceed [Riddihough, Nature 370 (1994) 78].

Regulation of DNA replication in irradiated cells by trans-acting factors

We compared DNA replication activity in cytoplasmic extracts prepared from irradiated and nonirradiated HeLa cells using a simian virus 40 (SV40)-based in vitro replication assay. The assay measures semi-conservative DNA replication in a plasmid carrying the SV40 origin of replication and requires SV40 T antigen as the sole noncellular protein. The plasmid DNA used in the replication reaction is never exposed to radiation. We find that replication of plasmid DNA is significantly reduced when cytoplasmic extracts from irradiated cells are used. Since plasmid replication proceeds to completion in extracts from irradiated cells, the observed reduction in the over-all replication activity is probably due to a reduction in the efficiency of initiation events. The degree of inhibition of DNA replication after exposure to 10, 30 and 50 Gy X rays as measured in vitro using this assay is similar to that measured in intact cells immediately before processing for extract preparation. These observations are compatible with the induction or activation by ionizing radiation of a factor(s) that inhibits in trans DNA replication. The results contribute to our understanding of the mechanism(s) developed by the cells to regulate DNA replication when exposed to clastogenic agents. Such processes may be of significance in the restoration of DNA integrity, and may define yet another checkpoint operating during S at the level of clusters of replicons.

Universal catalytic domain structure of AdoMet-dependent methyltransferases

The DNA methyltransferases, M.HhaI and M.TaqI, and catechol O-methyl-transferase (COMT) catalyze the transfer of a methyl group from the cofactor S-adenosyl-L-methionine (AdoMet) to carbon-5 of cytosine, to nitrogen-6 of adenine, and to a hydroxyl group of catechol, respectively. The catalytic domains of the bilobal proteins, M.HhaI and M.TaqI, and the entire single domain of COMT have similar folding with an alpha/beta structure containing a mixed central beta-sheet. The functional residues are located in equivalent regions at the carboxyl ends of the parallel beta-strands. The cofactor binding sites are almost identical and the essential catalytic amino acids coincide. The comparable protein folding and the existence of equivalent amino acids in similar secondary and tertiary positions indicate that many (if not all) AdoMet-dependent methyltransferases have a common catalytic domain structure. This permits tertiary structure prediction of other DNA, RNA, protein, and small-molecule AdoMet-dependent methyltransferases from their amino acid sequences.

Effect of ionizing radiation on the expression of chloramphenicol acetyltransferase gene under the control of commonly used constitutive or inducible promoters

We examined the effect of ionizing radiation on the expression of the chloramphenicol acetyltransferase (CAT) gene driven by commonly used viral or semi-synthetic promoters in transient transfection assays using COS-7 cells. Specifically, we studied the constitutive early promoters of cytomegalovirus (CMV), Rous sarcoma virus (RSV), and the simian virus 40 (SV40), and the inducible promoters from mouse mammary tumour virus (MMTV, inducible by dexamethasone) and the semi-synthetic SVlacO promoter (SVlacO, inducible by isopropyl beta-D-thiogalactoside). CAT activity was measured in cells exposed to 20 Gy X-rays and in non-irradiated controls 46 h after transient transfection. We observed that CAT expression from the CMV and SV40 promoters remained unchanged in cells exposed to radiation. Similar results were obtained with MMTV and SVlacO promoters when cells were irradiated 16 h after induction. However, expression from the RSV promoter was significantly increased after radiation exposure and similar results were obtained with the MMTV and SVlacO promoters when irradiation immediately preceded induction. The results suggest a classification of promoters as radiation-independent and -dependent. The constitutive CMV and SV40 promoters belong to the first category, whereas RSV belongs to the second category. The inducible MMTV and SVlacO promoters would be classified to the first category when induction precedes irradiation by 16 h, and to the second category when irradiation immediately follows induction. It will be desirable to use promoters under conditions that classify them to the first category to study the effect on cellular response to radiation of genes suspected to influence the intrinsic radiosensitivity of cells.

Interface for a four-sector mass spectrometer with a dual-purpose collision cell: High transmission at low to intermediate energies

A new interface system that consists of an ion decelerator, a floating collision cell-chemical ionization ion source, and an ion extractor was designed and installed in the third field-free region of a four-sector tandem mass spectrometer. Important features include the use of cylindrical deceleration lenses and an extraction lens assembly. This new design was found to provide enhancement of ion transmission at low to intermediate ion kinetic energies (3 eV to 1 keV) compared with the standard collision cell design. Collision-induced dissociation experiments from 3 eV to 10 keV and ion-molecule reactions of mass-selected ions can be performed conveniently. A second, grounded, collision cell is located after the extraction lenses, which allows MS(4) experiments to be carried out via the normal linked (B/E) scan function in MS2. Incorporation of chemical ionization capability into the electrically isolated collision cell makes it possible to carry out neutralization chemical-reionization mass spectrometry.

Crystal structure of casein kinase-1, a phosphate-directed protein kinase

The structure of a truncated variant of casein kinase-1 from Schizosaccharomyces pombe, has been determined in complex with MgATP at 2.0 A resolution. The model resembles the 'closed', ATP-bound conformations of the cyclin-dependent kinase 2 and the cAMP-dependent protein kinase, with clear differences in the structure of surface loops that impart unique features to casein kinase-1. The structure is of unphosphorylated, active conformation of casein kinase-1 and the peptide-binding site is fully accessible to substrate.

DNA modification by methyltransferases

Enzymatic methylation of DNA plays important roles in both prokaryotes and eukaryotes. Structural study of the HhaI DNA methyltransferase has provided considerable insight into the chemistry of C5-cytosine methylation. The DNA-protein complex reveals a substrate cytosine flipped out of the double helix during the reaction, and a novel two-loop DNA-binding motif used for both sequence recognition and flipping the base. Structural comparison of HhaI C5-cytosine methyltransferase, TaqI N6-adenine methyltransferase, and catechol O-methyltransferase reveals a common catalytic domain structure, which might be universal among S-adenosyl-L-methionine (SAM)-dependent methyltransferases.

[Isolation and identification of enteric adenovirus in China]

Enteric adenovirus type 40/41 is considered to be the second major cause of gastroenteritis in young children. In this study fecal specimens 86-123 from diarrhea patients were isolated and examined in Grahm 293 cells. This induced cytopathic effect (CPE) at this cells. Viral particles were also found in fecal specimens and by electron microscopy. Examination of the isolate with Cambridge Biotech Adenoclone-Type 40/41 test kit indicated that it contained EAd. On the basis of the above studies, one strain of EAd was the first isolated virus in China.

Ossification processes and perichondral ossification groove of Ranvier: a morphological study in developing human calcaneus and talus

In this histologic-radiologic investigation of 32 feet of 16 fetuses and newborns ranging in age from 15 to 44 weeks, two types of ossification, i.e., endochondral ossification through primary ossification center and intramembraneous ossification through periosteal bone formation (PBF), were found to coexist in both calcaneus and talus. In addition, Ranvier's grooves (RG), or perichondral ossification groove, also was observed as a shallow, saucer-like or semicircular structure. As with PBFs, there are three and two RGs in the calcaneus and talus, respectively. RG and PBF appeared in time order and were located regularly in the concave areas of the adult calcaneus and talus. The findings support the hypothesis that one function of PBF and RG is to limit the growth of the calcaneus and talus. Thus, they are responsible for the irregular contour of the calcaneus and talus.

Bio-affinity characterization mass spectrometry

A new approach, bio-affinity characterization mass spectrometry (BACMS), aimed at providing a more rapid, sensitive and potentially more flexible alternative to techniques presently employed for the characterization of noncovalent interactions in mixtures, such as would be encountered in combinatorial chemistry, in presented. BACMS avoids some of the difficulties and potential artifacts associated with affinity chromatography since the noncovalent associations occur in solution; thus, BACMS avoids the requirement of solid support media and the development of non-interfering linker species. This paper describes the conceptual basis for the methodology and its potential use in applications which include the screening of high affinity ligands in support of new drug development. BACMS exploits new Fourier-transform ion cyclotron resonance (FTICR) mass spectrometry technologies which, when coupled to electrospray ionization (ESI), allow the investigation of specific noncovalent complexes formed in solution. BACMS utilizes the well-known attributes of FTICR, such as the high resolution mass analysis and (MS)n (n > or = 2) capabilities; however, it is even more directly a result of recently developed techniques involving quadrupolar excitation, such as selected-ion accumulation. These tools are demonstrated and the results illustrate the extraordinary sensitivity achievable (solution concentration of 1 x 10-9 M without the use of separations prior to ESI). Thus, the new capabilities demonstrated here, in conjunction with ESI, will be useful for the investigation of very low relative concentration noncovalent association directly from solution, and promote a faster alternative for combinatorial mixture screening and analysis.

Vascular pharmacology of methylene blue in vitro and in vivo: a comparison with NG-nitro-L-arginine and diphenyleneiodonium

1. The vascular effects of the soluble guanylyl cyclase inhibitor, methylene blue as well as the nitric oxide (NO) synthase inhibitors, NG-nitro-L-arginine (L-NOARG) and diphenyleneiodonium (DPI) were studied in rat isolated aortic rings and conscious, unrestrained rats. 2. Acetylcholine (ACh) and sodium nitroprusside (SNP) caused concentration-dependent relaxation of preconstricted aortic rings. Both methylene blue (1 x 10(-5) M) and L-NOARG (3 x 10(-5) M) abolished ACh-induced relaxation; however, methylene blue but not L-NOARG shifted the concentration-response curve of SNP to the right. 3. In conscious rats, i.v. infusion of methylene blue (1.1 x 10(-5) mol kg-1 min-1), at a concentration which reduced the aortic tissue level of cyclic GMP by 50%, did not significantly alter mean arterial pressure (MAP) and heart rate (HR). In contrast, i.v. bolus injection of L-NOARG (1.5 x 10(-4) mol kg-1) markedly increased MAP and decreased HR. 4. Both ACh and SNP dose-dependently decreased MAP in conscious rats. Methylene blue did not alter the magnitude or duration of ACh- or SNP-induced depressor responses. L-NOARG, on the other hand, significantly though incompletely, reduced the magnitude and duration of the depressor response to ACh but not SNP. The depressor response to ACh or SNP was not altered by pretreatment with indomethacin (1.4 x 10(-5) mol kg-1) or capsaicin (3.3 x 10(-4) mol kg-1). 5. NG-nitro-L-arginine methyl ester (L-NAME) also caused dose-dependent increases in MAP in conscious rats. Both methylene blue and DPI (1 x 10-5 mol kg-1) selectively shifted the dose-pressor response curve of L-NAME to the right.6. These results suggest that: (1) the inhibition of endogenous NO biosynthesis does not necessarily lead to pressor response in vivo, (2) L-NOARG may not produce pressor response solely via the inhibition of endogenous endothelial NO biosynthesis, and (3) the depressor responses to ACh and SNP may not involve the release of NO or prostanoids or afferent nerve transmitters.

Absolute requirement of cyclic nucleotide in the activation of the G141Q mutant cAMP receptor protein from Escherichia coli

cAMP receptor protein (CRP), when interacting with cAMP, controls the expression of a network of catabolite-sensitive genes in Escherichia coli. To understand the molecular events that lead to the activation of CRP, a combined approach of site-directed mutagenesis and thermodynamic analysis was employed to study a member of a specific class of CRP mutant, CRP, which activates the in vivo expression of CRP-dependent operons in cya- strains in the absence of exogenous cAMP. Results from in vitro studies show that the CRP mutant G141Q absolutely requires cAMP for interacting with specific DNA. A quantitative comparison of the thermodynamic parameters governing ligand binding and DNA-protein complex formation in the presence of different cyclic nucleotides leads to the conclusion that this CRP mutant is activated only in the presence of cyclic nucleotides. The specificity toward cyclic nucleotides exhibited by wild-type CRP is lost in this mutant. Furthermore, the binding affinity of the ligand for the first binding site of the mutant is essentially the same as that of wild-type CRP regardless of the identity of the cyclic nucleotide. Hence, the observed in vivo activation of CRP-dependent operons by G141Q in the absence of exogenous cAMP is most likely the consequence of the replacement of cAMP by other cyclic nucleotides to activate the mutant. It is also possible that trace levels of cAMP present in the cya- strain could account for the in vivo activation of the mutant. Furthermore, these results indicate that this CRP mutant does not assume the activated conformation in the absence of cyclic nucleotides, in contrast to the current model derived from results of in vivo studies.

Effects of liuwei dihuang wan [symbol: see text:bd and some other TCM drugs on bone biomechanics and serum 25 (OH)D3 content in rats

After a relatively long-term injection of hydrocortisone into rats, the strength of bone (anti-stress capacity) reduced evidently, while the rigidity (anti-deformity capacity) increased markedly (ie, bone fragility elevated). At the same time, the content of serum 25(OH)D3 decreased remarkably. After oral administration of Liuwei Dihuang Wan ([see symbol: see text]), anti-stress capability of bone increased evidently and its anti-deformity capability returned to normal; however, there was no elevation of serum 25(OH)D3 content. The effect of Longmu Zhuanggu Chongji ([see symbol: see text]) or Jisheng Shenqi Wan (see symbol: see text]) was lower than that of Liuwei Dihuang Wan. The experiments suggests that Liuwei Dihuang Wan is beneficial to preventing and curing osteoporosis, but no correlation between its mechanism and the metabolism of 25(OH)D3 was demonstrated.

Structure of PvuII endonuclease with cognate DNA

We have determined the structure of PvuII endonuclease complexed with cognate DNA by X-ray crystallography. The DNA substrate is bound with a single homodimeric protein, each subunit of which reveals three structural regions. The catalytic region strongly resembles structures of other restriction endonucleases, even though these regions have dissimilar primary sequences. Comparison of the active site with those of EcoRV and EcoRI endonucleases reveals a conserved triplet sequence close to the reactive phosphodiester group and a conserved acidic pair that may represent the ligands for the catalytic cofactor Mg2+. The DNA duplex is not significantly bent and maintains a B-DNA-like conformation. The subunit interface region of the homodimeric protein consists of a pseudo-three-helix bundle. Direct contacts between the protein and the base pairs of the PvuII recognition site occur exclusively in the major groove through two antiparallel beta strands from the sequence recognition region of the protein. Water-mediated contacts are made in the minor grooves to central bases of the site. If restriction enzymes do share a common ancestor, as has been proposed, their catalytic regions have been very strongly conserved, while their subunit interfaces and DNA sequence recognition regions have undergone remarkable structural variation.

Charge-state shifting of individual multiply-charged ions of bovine albumin dimer and molecular weight determination using an individual-ion approach

Ion-molecule reactions of individual multiply-protonated ions of bovine albumin dimer, formed from electrospray ionization, have been studied using a Fourier transform ion cyclotron resonance mass spectrometer. Upon reaction of ammonia with a group of individual ions, charge-state shifting was observed due to proton transfer. Repeated additions of ammonia during remeasurements of the same ion population were observed to induce multiple-step charge-state shifts. Charge-state-dependent reactivity, as well as nonstatistical behavior in reactivity, was observed due to the small ion population. The molecular weights of individual ions whose charge state shifted during reaction were determined with an accuracy of 67 ppm, the first example of using an individual-ion approach to the determination of molecular weight for a large biopolymer. The molecular weight distribution of a group of ions can be determined with a precision related to the number of ions examined and the weight heterogeneity of the sample. We obtained the molecular weight for eight individual ions from which a molecular weight of 133,320 +/- 210 Da was calculated for bovine albumin dimer.

[Evaluation of the clinical acute electrophysiological effects of propafenone using transesophageal atrial pacing]

The clinical acute electrophysiological effects of propafenone were evaluated using transesophageal atrial pacing (TEAP) in 65 patients with various arrhythmias. The mean age of the patients was 41 years. Incremental pacing and programmed ectopic stimulation were performed on each patient before and during drug administration. Propafenone was given as a bolus injection of 1.5mg.kg-1 body weight followed by drip infusion at a rate of 1 mg.min-1. S-R, P wave, P-R and QRS intervals were prolonged from 194.43 +/- 21.59, 97.49 +/- 10.92, 148.00 +/- 16.20 and 82.21 +/- 7.18ms 223.00 +/- 29.25, 100.22 +/- 10.60, 166.60 +/- 20.10 and 86.54 +/- 7.19ms, respectively (P < 0.005), A-V conduction system effective refractory period (AVCSERP) was prolonged from 316.35 +/- 82.97ms to 360.31 +/- 82.67ms (P < 0.0001) in the treated group. There was no change of atrial ERP and QTc interval (P > 0.05). Fast and slow pathway ERP was prolonged by 13% and 28% of the control value, respectively (P < 0.015), and accessory pathway ERP was prolonged from 278.89 +/- 27.13ms to 305.56 +/- 33.58ms (P < 0.001), in the treated group. Sinus cycle length, corrected sinus nodal recovery time and total sinus-atrial conductive time were significantly prolonged (P < 0.0001). The results can partially explain the antiarrhythmic effects and the side effects of propafenone. TEAP is dependable in evaluating the clinical electrophysiological effects of drugs.

Analysis of the humoral response elicited in mice by a chimeric peptide representing variable segments I and IV of the major outer membrane protein of Chlamydia trachomatis

A synthetic chimeric peptide representing the variable segments I (VS I) and IV of the major outer membrane protein (MOMP) of Chlamydia trachomatis, serovars C and E respectively, was studied to determine its ability to elicit a neutralizing humoral response in mice. Antibody responses varied to the peptide in the five inbred strains of mice, A/J(H-2a), DBA/1(H-2q), C57BL/10(H-2b), CBA/J(H-2k), Balb/c(H-2d), that were immunized. There was a spectrum of antibody responses which ranged from high ELISA and IFA titres by the C57BL/10 mice to little or no response by Balb/c mice. Antisera from C57BL/10 mice recognized all 15 serovars of C. trachomatis in a dot blot assay. A pepscan of the antisera from C57BL/10 mice showed strong reactivity to both neutralizing epitopes VAGLQNDPT in VS I of serovar C and the species-conserved peptide, TLNPTIA, in the VS IV. This antiserum neutralized, in vitro, the infectivity of serovars representing the B complex (B, D and E), C complex (C and J), B-related (F) and C-related (L3) complexes. In an attempt to elicit a stronger response to the peptide in the weakly reactive Balb/c and the DBA/1 strains, the peptide was conjugated to the carrier, keyhole limpet haemocyanin (KLH). All mice immunized with the KLH-peptide produced high-titred antisera that recognized neutralizing epitopes in VS I and VS IV and strongly neutralized the infectivity of both serovars C and E.

The structure of bacteriophage T7 lysozyme, a zinc amidase and an inhibitor of T7 RNA polymerase

The lysozyme of bacteriophage T7 is a bifunctional protein that cuts amide bonds in the bacterial cell wall and binds to and inhibits transcription by T7 RNA polymerase. The structure of a mutant T7 lysozyme has been determined by x-ray crystallography and refined at 2.2-A resolution. The protein folds into an alpha/beta-sheet structure that has a prominent cleft. A zinc atom is located in the cleft, bound directly to three amino acids and, through a water molecule, to a fourth. Zinc is required for amidase activity but not for inhibition of T7 RNA polymerase. Alignment of the zinc ligands of T7 lysozyme with those of carboxypeptidase A and thermolysin suggests structural similarity among the catalytic sites for the amidase and these zinc proteases. Mutational analysis identified presumed catalytic residues for amidase activity within the cleft and a surface that appears to be the site of binding to T7 RNA polymerase. Binding of T7 RNA polymerase inhibits amidase activity.

Identification of serotype 1-, 3-, and 6-specific antigens of Ureaplasma urealyticum by using monoclonal antibodies

Little is known about the antigens responsible for serotype specificity in Ureaplasma urealyticum. We produced monoclonal antibodies to U. urealyticum serotypes 1, 3, and 6, the serotypes most commonly found in pregnant women, and analyzed serotype-specific antigens for the three serotypes. Clinical isolates belonging to serotype 1, 3, or 6 were tested in immunoblots with these monoclonal antibodies. The immunoblot patterns of these isolates were, in most cases, different from each other as well as from those of the reference strains, indicating a high rate of antigenic variation among U. urealyticum strains.