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At least 1,135 records · Page 63Linked to original sources
PubMed1983

Enzymatic construction and selection of bacteriophage G4 mutants with modifications of a DNA secondary structure in the J-F intercistronic region.

The J-F intercistronic region of bacteriophage G4 has the potential to form a perfectly base-paired hairpin structure, thought to act as a terminator of transcription. To investigate this proposed structure-function relationship, viable mutants were constructed by site-specific mutagenesis with small deletions of 2 to 4 base pairs in the center of the corresponding palindromic sequence. These sequence modifications had a small positive effect on the growth efficiency of the phage. The approach of biochemical rather than biological selection of these mutant phages is generally applicable to the construction of virus and plasmid vectors.

Base Sequence↗
PubMed2003

Spore-specific modification of DNA-dependent RNA polymerase alpha subunit in streptomycetes--a new model of transcription regulation.

At the very beginning of spore germination in streptomycetes the full-length alpha subunit of DNA-dependent RNA polymerase is shortened from its C-terminus. The C-terminal domain of the protein is required for binding of DNA and transcription regulators but its regulatory role in streptomycetes was not extensively studied. Comparison of the sequences of E. coli and S. coelicolor RNA polymerase alpha subunit (RNAP alpha) C-terminal domains reveals that the majority of amino acid residues responsible for the interaction with transcription regulators is conserved in both microorganisms. The spore specific modification of streptomycete RNAP alpha could thus have its regulatory role. The nature of the proteolytic enzyme, responsible for the RNAP alpha cleavage is discussed.

DNA-Directed RNA Polymerases↗
PubMed1992

Biological function of DNA methylation.

Structural and functional properties of prokaryotic DNA methyltransferases are summarized. The different aspects of the role of DNA methylation which influences DNA-protein interaction in restriction and modification of DNA and in mismatch repair, DNA replication and gene expression are discussed.

Bacteria↗
PubMed1997

Glyceraldehyde 3-phosphate-induced DNA or protein modifications severely inhibit the protein/DNA interaction.

In this study, the effect of the reducing sugar glyceraldehyde 3-phosphate on protein/DNA interaction has been investigated. Treatment with glyceraldehyde 3-phosphate of oligonucleotides recognized by various transcription factors severely inhibits protein binding. The inhibitory effect is time and dose-dependent. Treatment with glyceraldehyde 3-phosphate of the homeodomain protein TTF-1 HD has also an inhibitory effect on the interaction with DNA, again in a time and dose-dependent manner. These "in vitro" effects could have "in vivo" counterparts and therefore contribute to molecular alterations observed either when intracellular protein are exposed to high doses of reducing sugars (i.e. in diabetes) or after a long time exposure (i.e. in Gzero-arrested cells during aging).

Animals↗
PubMed1995

[Cooperative interactions of oligodeoxyribonucleotides upon binding with DNA by chemical modification].

Quantitative characteristics of the modification of deoxyribooligonucleotide TTGCCTTGAATGG-GAAGAGGGTCATT (P) with 4-(N-2-chloroethyl-N-methylamino)benzyl phosphamide derivative of oligonucleotide pTTCCCA (X) were studied. The modification was performed in the presence of derivatives of the oligonucleotides (Phn-L)pTTCAAGGCp(L-Phn) (E1) and (Phn-L)pTGACCCTCp(L-Phn) (E2), where Phn is the residue of N-(2-hydroxyethyl)phenazinium, and L is ethylene diamine spacer. In PXE1, PXE2, and PXE1E2 complexes, E1, E2, and reagent X are bound with target P in tandem, with E1 near the 3'-end and E2 near the 5'-end of the reagent X. From the dependences of the maximum in time modification degree of target P and the shorter targets containing the complementary binding site for the reagent X on its concentration, the association constants of the complexes PX, PE1, and PE2 were determined as Kx = (4.2 +/- 0.6) x 10(4) M-1, Ke1 = (1.25 +/- 0.44) x 10(7) M-1, and Ke2 = (2.56 +/- 1.22) x 10(6) M-1, respectively. The cooperativity coefficients of joint binding the X, E1, and E2 with the target giving rise to the complexes PXE1, PXE2, and PXE1E2 were estimated as alpha 1 = 15.7 +/- 2.1, alpha 2 = 8.7 +/- 1.2, and alpha 12 = 136.5 +/- 2.6, respectively. The data obtained suggest that E2 is not only the effector of modification but it is also an inhibitor due to the formation of the complex PE2* with Ke2* = (1.97 +/- 1.27) x 10(7) M-1 not capable of adding the reagent X.

Base Sequence↗
PubMed1975

The modification of DNA-dependent RNA polymerase from Escherichia coli by an alkylating derivative of rifamycin SV.

3-(2-Bromo[1-14C]acetamidoethyl)-thio-rifamycin SV, abbreviated BrAcNEtS-Rif, and alkylating derivative of rifamycin SV was synthesized. A four-fold excess of BrAcNEtS-Rif inhibited the enzymic activity of RNA polymerase from Escherichia coli to 97%. Incubation of RNA polymerase with Br[14C]AcNEtS-Rif led to covalent substitution. The reaction of Br[14C]AcNEtS-Rif with enzyme at a ratio of 1.4:1 and a concentration of 63 nM was found to proceed with a half life of 1 h at 37 degrees C. The enzyme could be protected from reaction with BrAcNEtS-Rif by either rifampicin or the hybrid [poly(dT)]-[r(Ap)5a]. The modification of holoenzyme by Br[14C]AcNEtS-Rif in the presence of p-hydroxymercuribenzene sulfonic acid (pOH-HgBzSO3H) or 4 M LiCl occurred with faster kinetics and led to a higher degree of substitution. Reaction of Br[14C]AcNEtS-Rif with RNA polymerase core enzyme caused predominant substitution of subunit beta. In the case of RNA polymerase holenzyme the radioactive substituents were evenly distributed between subunits beta and sigma. Apparently the topology of the rifamycin binding site of holoenzyme, similarly to core enzyme, precludes attacks of nucleophilic functions from beta' and alpha, but it allows nucleophilic functions from subunits beta and sigma to react with equal probability on BrAcNEtS-Rif. In the presence of a 20-fold excess of pOH-HgBzSO3H, the modification of holoenzyme was drastically altered. Virtually all substitution took place on subunit beta', very little on beta and none on subunits sigma and alpha.

Alkylating Agents↗
PubMed1976

Evidence for host-dependent modification and restriction of bacteriophage DNA in Mycobacterium tuberculosis.

Wild isolates of Mycobacterium tuberculosis may be divided into the three internationally recognized phage types on the basis of susceptibility to mycobacteriophages DS6A, BK1 and D34. Strains of type A are lysed at high efficiency by DS6A only; type B is lysed by BK1 grown on Mycobacterium smegmatis ATCC607 and DS6A, while type C is lysed additionally by D34 grown on atypical Mycobacterium F130. Propagation of D34 on a C-strain (D34-C) or BK1 on a B-strain (BK1-B) has no effect on viral host-range. D34-C has an efficiency of plating (e.o.p.) of 10(-5) on type B strains and 10(-7) on A strains. BK1-B plates on A strains at an e.o.p. of 10(-5). BK1 recovered from and repropagated on an A strain (BK1-A) has an e.o.p. of 1-0 on strains of all classes. D34-B has an e.o.p. of 1-0 on strains of type B and C, while D34-A plates with high efficiency on types B and C and displayed an e.o.p. of 10(-4) on type A. Repropagation of these viruses on the M. tuberculosis strains originally lysed by them results in the restoration of their previous host range. Variations in plating efficiency cannot be explained by differences in viral absorption alone. These findings suggest that the three phage types of human tubercle bacilli are related by a hierarchical pattern of DNA restriction and modification in which the C pattern is included in the B, and both patterns are included in A-modified DNA. Viruses such as DS6A which are equally virulent for strains of all classes are not susceptible to host dependent restriction.

Bacteriophage Typing↗
PubMed1988

Diethyl pyrocarbonate reaction with the lactose repressor protein affects both inducer and DNA binding.

Modification of the lactose repressor protein of Escherichia coli with diethyl pyrocarbonate (DPC) results in decreased inducer binding as well as operator and nonspecific DNA binding. Spectrophotometric measurements indicated a maximum of three histidines per subunit was modified, and quantitation of lysine residues with trinitrobenzenesulfonate revealed the modification of one lysine residue. The loss of DNA binding, both operator and nonspecific, was correlated with histidine modification; removal of the carbethoxy groups from the histidines by hydroxylamine was accompanied by significant recovery of DNA binding function. The presence of inducing sugars during the DPC reaction had no effect on histidine modification or the loss of DNA binding activity. In contrast, inducer binding was not recovered upon reversal of the histidine modification. However, the presence of inducer during reaction protected lysine from reaction and also prevented the decrease in inducer binding; these results indicate that reaction of the lysine residue(s) may correlate to the loss of sugar binding activity. Since no difference in incorporation of radiolabeled carbethoxy was observed following reaction with diethyl pyrocarbonate in the presence or absence of inducer, the reagent appears to function as a catalyst in the modification of the lysine. The formation of an amide bond between the affected lysine and a nearby carboxylic acid moiety provides a possible mechanism for the activity loss. Reaction of the isolated NH2-terminal domain resulted in loss of DNA binding with modification of the single histidine at position 29. Results from the modification of core domain paralleled observations with intact repressor.

Bacteriophage lambda↗
PubMed2000

Transfer RNA modification, temperature and DNA superhelicity have a common target in the regulatory network of the virulence of Shigella flexneri: the expression of the virF gene.

Full expression of the virulence genes of Shigella flexneri requires the presence of two modified nucleosides in the tRNA [queuosine, Q34, present in the wobble position (position 34) and 2-methylthio-N6-isopentenyladenosine (ms2i6A37, adjacent to and 3' of the anticodon)]. The synthesis of these two nucleosides depends on the products of the tgt and miaA genes respectively. We have shown that the intracellular concentration of the virulence-related transcriptional regulator VirF is reduced in the absence of either of these modified nucleosides. The intracellular concentration of VirF is correlated with the expression of the virulence genes. Overproduction of VirF in the tgt and the miaA mutants suppressed the less virulent (tgt) or the avirulent (miaA) phenotypes respectively, caused by the tRNA modification deficiency. This suggests that the primary result of undermodification of the tRNA is a poor translation of virF mRNA and not of any other mRNA whose product acts downstream of the action of VirF. Shigella showed no virulence phenotypes at 30 degrees C, but forced synthesis of VirF at 30 degrees C induced the virulence phenotype at this low temperature. In addition, removal of the known gene silencer H-NS by a mutation in its structural gene hns increased the synthesis of VirF at low temperature and thus induced a virulent phenotype at 30 degrees C. Conversely, decreased expression of VirF at 37 degrees C induced by the addition of novobiocin, a known inhibitor of gyrase, led to an avirulent phenotype. We conclude that tRNA modification, temperature and superhelicity have the same target - the expression of VirF - to influence the expression of the central regulatory gene virB and thereby the virulence of Shigella. These results further strengthen the suggestion that the concentration of VirF is the critical factor in the regulation of virulence in Shigella. In addition, they emphasize the role of the bacterial translational machinery in the regulation of the expression of virulence genes which appears here quantitatively as important as the well-established regulation on the transcriptional level.

Antigens, Bacterial↗
PubMed1992

Selective inhibition of the BPDE-I-induced modification of the replicating DNA of S-phase cells, by benzamide and 3-aminobenzamide.

Treatment of human skin fibroblasts in early S-phase with (+-)7 beta,8 alpha-dihydroxy-9 alpha,10 alpha-epoxy-7,8,9,10- tetrahydrobenzo[a]pyrene (BPDE-I) results in more extensive modification of early replicating DNA than parental DNA. We have investigated the effects of benzamide (BZ) and 3-aminobenzamide (3-ABZ), inhibitors of transformation, on the modification of parental and replicating DNA of cells in early S-phase by BPDE-I. Synchronized cells were exposed to 5-bromodeoxyuridine at S-phase entry and treated 3 h later with 0.114 microM BPDE-I for 30 min. The cells at the time of treatment represent a radiolabeling index of 40 +/- 5% of the total number of cells. The replicated DNA was isolated from the non-replicated parental DNA on a CsCl gradient. A 32P-postlabeling procedure was used to quantitate the carcinogen-DNA adducts. The level of modification per nucleotide residue of the early replicated DNA was 1.6-2.2 times higher compared to the level of modification of the parental DNA. Addition of BZ inhibited the BPDE-I modification of the replicated DNA by 27-53%. There was no significant effect on the parental DNA modification. The major adduct that was quantitatively suppressed in the early replicated DNA was BPDE-I-trans-N2-dG. The addition of 3-ABZ also inhibited the modification of the dG by approximately 50% without significantly inhibiting the BPDE-I-dG adducts in the parental DNA. The data suggest that BZ and 3-ABZ inhibit the modification of specific sites in the replicating DNA leading to inhibition of transformation.

Benzamides↗
PubMed2005

Novel relationships among DNA methylation, histone modifications and gene expression in Ascobolus.

By studying Ascobolus strains methylated in various portions of the native met2 gene or of the hph transgene, we generalized our previous observation that methylation of the downstream portion of a gene promotes its stable silencing and triggers the production of truncated transcripts which rarely extend through the methylated region. In contrast, methylation of the promoter region does not promote efficient gene silencing. The chromatin state of met2 methylated strains was investigated after partial micrococcal nuclease (MNase) digestion. We show that MNase sensitive sites present along the unmethylated regions are no longer observed along the methylated ones. These chromatin changes are not resulting from the absence of transcription. They are associated, in both met2 and hph, with modifications of core histones corresponding, on the N terminus of histone H3, to an increase of dimethylation of lysine 9 and a decrease of dimethylation of lysine 4. Contrary to other organisms, these changes are independent of the transcriptional state of the genes, and furthermore, no decrease in acetylation of histone H4 is observed in silenced genes.

Acetylation↗
PubMed1976

DNA restriction and modification systems in Salmonella. SQ, a new system derived by recombination between the SB system of Salmonella typhimurium and the SP system of Salmonella potsdam.

As the result of P1-mediated cotransduction with serB from Salmonella potsdam to the Escherichia coli/Salmonella typhimurium hybird 4617, one recombinant, L4004, was isolated which had a restriction-modification (R--M) system different from the SB and SP systems of its parents, and was designated SQ. The genes of SQ were allelic to those of the SB system of S. typhimurium and were shown by complementation experiments to be functionally related to those of the K system of E. coli. Evidence that the SQ system in L4004 arose as the result of a recombination event within the hsdS genes of SB and SP is discussed.

Alleles↗
PubMed1976

Measurement of DNA antibodies.

Modifications of the standard Farr technic for assaying DNA antibodies are presented; these result in improved separation of normals from abnormals, enhanced reproducibility, and simplicity of performance. The use of 0.4 M borate buffer extends the range of the assay, while a 0.1 M buffer aids differentiation when equivocal results are obtained. Centrifugation of vials prior to counting improves the reproducibility by approximately 3%. Polyethylene glycol, at a final concentration of 6 Gm. per 100 ml., can be substituted for ammonium sulfate, with some advantages.

Antibodies↗
PubMed2003

Mammalian epigenomics: reprogramming the genome for development and therapy.

Epigenetic modifications of DNA and chromatin are important for genome function during development and in adults. DNA and chromatin modifications have central importance for genomic imprinting and other aspects of epigenetic control of gene expression. In somatic lineages, modifications are generally stably maintained and are characteristic of different specialized tissues. The mammalian genome undergoes major reprogramming of modification patterns in germ cells and in the early embryo. Some of the factors that are involved both in maintenance and in reprogramming, such as methyltransferases, are being identified. Epigenetic reprogramming is deficient in animal cloning, which is a major explanation for the inefficiency of the cloning procedure. Deficiencies in reprogramming are likely to underlie the occurrence of epimutations and of epigenetic inheritance. Environmental factors can alter epigenetic modifications and may thus have long-lasting effects on phenotype. Epigenomics methods are being developed to catalogue genome modifications under normal and pathological conditions. Epigenetic engineering is likely to play an important role in medicine in the future.

Animals↗
PubMed1980

DNA restriction and modification in Escherichia coli: functional analysis of the role of the dnaC(D) gene product.

Escherichia coli strain PC-7 carries two independent temperature-sensitive mutations, one affecting the restriction and modification (R-M) phenotype and the other the DnaC(D) phenotype. The results of complementation and P1 transduction analysis of the mutation affecting the R-M phenotype implicate a fourth gene, designated hsdX, located close to the hsd three-gene complex. The properties of merodiploids constructed between appropriate recipients and F' elements with different mutations in hsdS, hsdR and hsdM genes might indicate that in strain PC-7 the temperature-sensitive products, determined by hsdR and hsdSK cistrons, are synthesized. The role of the temperature-sensitive dnaC(D) gene product in the formation of the restriction endonuclease was studied and no direct relation was found between the DnaC(D) and R-M phenotypes.

DNA Replication↗
PubMed1982

[Directed modification of the damaged DNA region in inducing structural chromosomal mutations].

The method of directed modification of damaged DNA regions elaborated recently in our laboratory made it possible to conduct a direct experimental study of mutagenicity of two single-stranded breaks located within the isolocus of sister chromatids, in strands of the same polarity. The efficiency of induced mutagenesis was shown to be very high when the experimental technique was employed allowing single-stranded DNA breaks to occur in this position with high probability. It should be noted that the fraction of interstitial deletions and rearrangements of chromosomes of the exchange type were predominant in the spectrum of induced mutations. It is concluded that the coincidence of two breaks in the strands of the same polarity in the isolocus of sister chromatids is realised into chromosome aberrations with high probability.

Animals↗
PubMed1999

Chlorella viruses as a source of novel enzymes.

A special advantage has been conferred upon Chlorella cells as tools in biotechnology when viruses (Phycodnaviridae) infecting Chlorella cells were discovered and isolated. The viruses are large icosahedral particles (150-200 nm in diameter), containing a giant, 330-380 kbp long, linear dsDNA genome. Recently, the nucleotide sequence of the 330,740-bp genome of PBCV-1, the prototype virus of Phycodnaviridae, was determined, and up to 702 open reading frames (ORFs) were identified along the genome. The possible genes present include those encoding a variety of enzymes involved in the modification of DNA, RNA, protein and polysaccharides as well as those involved in the metabolism of sugars, amino acids, lipids, nucleotides and nucleosides. Many of these genes are actually expressed during viral infection, with functional enzymes detected in the host cytoplasm or incorporated into the virion. The successful utilization of these viral enzymes as various DNA restriction and modification enzymes (Cvi enzymes) that are now commercially available is well documented. Also noteworthy are virion-associated chitinase and chitosanase activities that have potentially important applications in the recycling of natural resources. The virions of Chlorella viruses contain more than 50 different structural proteins, ranging in size from 10 to 200 kDa. Some of these proteins may be replaced with useful foreign proteins using recombinant DNA technology. The proteins of interest can be recovered easily from the viral particles, and collected by centrifugation after complete lysis of the host Chlorella cells.

Journal Article↗