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PubMed2002

Structure of Alba: an archaeal chromatin protein modulated by acetylation.

Eukaryotic DNA is packaged into nucleosomes that regulate the accessibility of the genome to replication, transcription and repair factors. Chromatin accessibility is controlled by histone modifications including acetylation and methylation. Archaea possess eukary otic-like machineries for DNA replication, transcription and information processing. The conserved archaeal DNA binding protein Alba (formerly Sso10b) interacts with the silencing protein Sir2, which regulates Alba's DNA binding affinity by deacetylation of a lysine residue. We present the crystal structure of Alba from Sulfolobus solfataricus at 2.6 A resolution (PDB code 1h0x). The fold is reminiscent of the N-terminal DNA binding domain of DNase I and the C-terminal domain of initiation factor IF3. The Alba dimer has two extended beta-hairpins flanking a central body containing the acetylated lysine, Lys16, suggesting three main points of contact with the DNA. Fluorescence, calorimetry and electrophoresis data suggest a final binding stoichiometry of approximately 5 bp DNA per Alba dimer. We present a model for the Alba-DNA interaction consistent with the available structural, biophysical and electron microscopy data.

Acetylation↗
PubMed1979

31P NMR studies of the solution structure and dynamics of nucleosomes and DNA.

31P NMR studies of 140 base pair DNA fragments in nucleosomes and free in solution show no detectable change in the internucleotide 31P chemical shift or linewidth when DNA is packaged into nucleosomes. Measurements of 31P spin-lattice relaxation times T1 and 31P-[H] nuclear Overhauser enhancements revealed internal motion with a correlation time of about 4 x 10(-10) sec in double helical DNA, both free in solution and bound to nucleosomal core proteins. This result implies greater dynamic mobility in double helical DNA than has previously been supposed.

Chromatin↗
PubMed1998

DNA analysis of temperate bacteriophage Aa(phi)23 isolated from actinobacillus actinomycetemcomitans.

The DNA of the temperate bacteriophage Aaphi23 isolated from the oral bacterium Actinobacillus actinomycetemcomitans was examined structurally both in the phage head and in the prophage. The DNA in phage particles comprises 44 kb linear molecules with a terminal redundancy of 1.6 kb, which represent circular permutations. Thus, DNA is packaged into phage heads by the headful mechanism. The Aaphi23 prophage is integrated into the host chromosome.

Aggregatibacter actinomycetemcomitans↗
PubMed1969

Defective bacteriophage PBSH in Bacillus subtilis. II. Intracellular development of the induced prophage.

Treatment of Bacillus subtilis strain 168 with mitomycin C caused induction of a defective prophage, PBSH. During induction, extensive deoxyribonucleic acid (DNA) synthesis took place. Concurrently, a change in marker frequency of the bacterial DNA was noticed. The frequency of only one marker, ade-16, the marker closest to the origin of the bacterial chromosome, was enhanced manyfold. DNA from whole phage particles transformed all bacterial markers at a frequency equal to that of DNA in the noninduced culture, except ade-16, the frequency of which was enhanced 30 to 100 times. Analysis of a double isotope experiment demonstrated that 14% of the phage DNA was derived from preinduction bacterial DNA. The other 86% of DNA in phage particles was DNA replicated after induction. Density label experiments with 5-bromodeoxyuridine showed that postinduction DNA synthesis took place preferentially at the origin region of the bacterial chromosome. Measurement of the molecular weight of DNA replicated after induction clearly showed that postinduction DNA replication is chromosomal. No evidence for prophage detachment and autonomous phage DNA replication was found. The data indicated that, after mitomycin C action, the bacterial chromosome under-went multiple reinitiation at the origin, while normal sequential DNA replication was stopped. The pool of replicated bacterial DNA was fragmented randomly. This DNA was packaged into PBSH particles which were released after cell lysis.

Bacillus subtilis↗
PubMed1994

Human immunodeficiency virus integrase directs integration to sites of severe DNA distortion within the nucleosome core.

We have examined the consequences of DNA distortion and specific histone-DNA contacts within the nucleosome for integration mediated by the human immunodeficiency virus (HIV)-encoded integrase enzyme. We find that sites of high-frequency integration cluster in the most severely deformed, kinked DNA regions within the nucleosome core. This may reflect either a preference for a wide major groove for association of the integrase or a requirement for target DNA distortion in the DNA strand transfer mechanism. Both the distortion and folding of the target DNA through packaging into nucleosomes may influence the selection of HIV integration sites within the chromosome.

Animals↗
PubMed2004

DNaseI hypersensitivity analysis of chromatin structure.

Transcriptionally inactive DNA is packaged into condensed chromatin such that it is unavailable to the transcription initiation complex. Activation of the silenced genes during processes such as differentiation first requires that the chromatin structure be remodeled into a transcriptionally permissive configuration, with the DNA "exposed" and accessible to transcription factors. The change in chromatin structure associated with transcriptional competence can be detected as increased sensitivity of the exposed DNA to digestion with DNaseI. This increased susceptibility is referred to as DnaseI-hypersensitivity. DNaseI hypersensitive sites are often located in the recognition sites for transcription factors, including promoters and enhancers. This chapter describes the protocols necessary to perform and analyze DNaseI hypersensitivity assays, a technique becoming increasingly important given the rapid advances in our understanding of the chromatin remodeling processes.

Blotting, Southern↗
PubMed1997

Software for DNA sequencing by hybridization.

Sequencing by hybridization (SBH) is a promising alternative approach to DNA sequencing and mutation detection. Analysis of the resolving power of SBH involves rather difficult combinatorial and probabilistic problems, and sometimes computer simulation is the only way to estimate the parameters and limitations of SBH experiments. This paper describes a software package, DNA-SPECTRUM, which allows one to analyze the resolving power and parameters of SBH. We also introduce the technique for visualizing multiple SBH reconstructions and describe applications of DNA-SPECTRUM to estimate various SBH parameters. DNA-SPECTRUM is available at http://www-hto.usc.edu/software/sbh/index. html.

Base Sequence↗
PubMed1990

Physical basis for detection of DNA double-strand breaks using neutral filter elution.

Results using neutral filter elution are difficult to explain if this method detects only DNA double-strand breaks (DSBs). In an attempt to understand neutral filter elution, the size of DNA pieces eluted from filters was measured using pulsed-field gel electrophoresis. Contrary to expectation, the size of the pieces was independent of radiation dose and time of elution, and much smaller (approximately 460 kb) than anticipated based on the expected number of DSBs induced. Shearing of the DNA molecule, the presence of nonspecific nucleases, and the influence of DNA-associated proteins were examined but could not explain our results. Consequently, we propose that cell lysis causes swelling of the DNA gel, and the exposed fraction of DNA on the surface of the gel is then sheared as the elution solution flows through the filter. We suggest that the rate of DNA elution measured using neutral filter elution is dependent upon the number of DSBs present, the composition of the eluting solution, especially with regard to the presence of molecules which can influence chromatin swelling on the filter, and the conformation or "packaging" of DNA before lysis.

Animals↗
PubMed1994

The herpes simplex virus type 1 particle: structure and molecular functions. Review article.

This review is a summary of our present knowledge with respect to the structure of the virion of herpes simplex virus type 1. The virion consists of a capsid into which the DNA is packaged, a tegument and an external envelope. The protein compositions of the structures outside the genome are described as well as the functions of individual proteins. Seven capsid proteins are identified, and two of them are mainly present in precursors of mature DNA-containing capsids. The protein components of the 150 hexamers and 12 pentamers in the icosahedral capsid are known. These capsomers all have a central channel and are connected by Y-shaped triplexes. In contrast to the capsid, the tegument has a less defined structure in which 11 proteins have been identified so far. Most of them are phosphorylated. Eleven virus-encoded glycoproteins are present in the envelope, and there may be a few more membrane proteins not yet identified. Functions of these glycoproteins include attachment to and penetration of the cellular membrane. The structural proteins, their functions, coding genes and localizations are listed in table form.

Capsid↗
PubMed1987

Comparison of the DNA sequences involved in replication and packaging of the filamentous phages IKe and Ff (M13, fd, and f1).

The product of gene II of the distantly related, filamentous, single-stranded DNA phages IKe and Ff (M13, fd, and f1) is the only phage-encoded protein that is required for the replication of their double-stranded replicative form DNA. With the aid of recombinant plasmids containing the origins of viral strand replication [(+)-origins] of both IKe and Ff, we demonstrated that initiation but not termination of viral strand replication by gene II protein is restricted to its cognate (+)-origin. If the (+)-origins of IKe and Ff are present in the same orientation, fusion origins are generated upon gene II protein-instructed replication as a result of initiation at one origin and termination at the other. These fusion origins are only functional in the presence of the gene II protein encoded by the phage from which the sequence lying at the 3' side of the gene II protein cleavage site is derived. The nucleotides that determine the specificity of the replication initiation process are located between positions +17 and +49, or +17 and +40, with respect to the gene II protein cleavage site of IKe and Ff, respectively. The DNA sequence that forms the recognition signal for cleavage by gene II protein is probably located within the sequence that starts 3 nucleotides before and terminates 17 nucleotides after the cleavage site. Efficient packaging by phage IKe of plasmid DNA strands that contain the morphogenetic signal of Ff, or vice versa, indicates that, despite their only partial homology, the morphogenetic signals of IKe and Ff are interchangeable.

Bacteriophages↗
PubMed1976

Genetic recombination of bacteriophage T7 DNA in vitro.

We have demonstrated recombination of bacteriophage T7 DNA in vitro. An extract of Escherichia coli B cells infected with wild-type T7(T7+) is incubated with mature DNA extracted from T7 phage. Packaging of the exogenous DNA within the phage head appears to be preceded by recombination of exogenously added DNA with DNA present in the extracts. In order to detect the recombination, we used an exogenous DNA bearing a marker (ss-) such that progeny phage which have packaged this marker are able to plate on Shigella sonnei D2 571-48, whereas T7+ phage present in the extracts do not. The recombinational process bears many of the characteristics of in vivo recombination. The exogenous DNA is not packaged intact but undergoes fragmentation to a length of about 3000 base pairs before being incorporated into a mature DNA molecule. If ss- DNA bearing an amber mutation is used in the assay, the frequency of amber+ progeny produced varies with the distance of the amber marker from the ss- marker. When DNA bearing three mutations is used in the reaction, phage heterozygous for the unselected marker are readily detected. Finally the products of phage genes 4 (DNA replication protein), 5(DNA polymerase), and 6(exonuclease), genes previously implicated in recombination in vivo, are required for the in vitro reaction.

Coliphages↗
PubMed2002

Antisense gene therapy of brain cancer with an artificial virus gene delivery system.

Therapeutic genes are delivered to the nuclear compartment of cancer cells following intravenous administration with a non-immunogenic "artificial virus" gene delivery system that uses receptor-specific monoclonal antibodies (MAb) to navigate the biological barriers between the blood and the nucleus of the cancer cell. Mice implanted with intracranial U87 human glial brain tumors are treated with a nonviral expression plasmid encoding antisense mRNA against the human epidermal growth factor receptor gene (EGFR). The plasmid DNA is packaged within the interior of polyethylene glycol-modified (PEGylated) immunoliposomes, and delivered to the brain tumor with MAbs that target the mouse transferrin receptor (TRFR) and the human insulin receptor (INSR). The mouse TRFR MAb enables transport across the tumor vasculature, which is of mouse brain origin, and the INSR MAb causes transport across the plasma membrane and the nuclear membrane of the human brain cancer cell. The lifespan of the mice treated weekly with an intravenous administration of the EGFR antisense gene therapy packaged within the artificial virus is increased 100% relative to mice treated either with a luciferase gene or with saline.

Animals↗
PubMed1986

Proteins from the prokaryotic nucleoid. A protein-protein cross-linking study on the quaternary structure of Escherichia coli DNA-binding protein NS (HU).

Escherichia coli DNA-binding proteins NS1, NS2 and NS (NS1 + NS2) react with the protein-protein bifunctional cross-linking reagents dimethylsuberimidate and dimethyladipimidate to yield oligomers up to hexamers. The former reagent, with the longer arm, is more efficient than the other shorter one. Both one- and two-dimensional gel electrophoreses show that the cross-linked trimers are homogeneous, while the dimers appear heterogeneous, suggesting that at least two types of dimers but geometrically equivalent trimers are formed. In the presence of DNA, the cross-linking reaction with either reagent yields fewer dimers and more of the larger products. The yield of cross-linked products of various sizes was determined for NS1, NS2 and NS as a function of the protein concentration (0.03-3000 microM). From the results obtained in these experiments, we derived a model of quaternary structure in which dimers and tetramers are predominant in very solutions of the proteins. Above a critical concentration (10-50 microM), interactions among tetramers become increasingly important, yielding octamers and perhaps larger products. Our data do not support a recently proposed model in which the DNA is packaged around a protein disc consisting of 8-10 NS dimers.

Bacterial Proteins↗
PubMed1992

DNA associations: packing calculations in A-, B-, and Z-DNA structures.

A detailed theoretical study has been carried out to examine the modes of DNA-DNA interactions on the basis of hard-sphere contact criteria. Two helices of identical structure and length are oriented side-by-side and their relative positions are controlled by translations along and rotations about specific axes. Short atomic contacts between pairs of atoms in the structures are assessed and contact-free configurations are compiled. The computed contact-free arrangements of A, B, and Z double helices are found to be remarkably similar to the packing motifs observed in DNA crystals and stretched fibers. Equally interesting in the study are the broad ranges of sterically acceptable arrangements that preserve the overall packing morphology of neighboring duplexes: Among the most notable morphological features in the helical complexes are extended "super" major and minor grooves which might facilitate the wrapping and packaging of DNA chains in supramolecular assemblies. The hard-sphere computations, however, are insufficient for quantitative interpretation of the packing of DNA helices in the solid state. The results are, nevertheless, a useful starting point for energy based studies as well as relevant to the analysis of long-range interactions in DNA supercoils and cruciforms.

DNA↗
PubMed2006

Latency-associated nuclear antigen (LANA) of Kaposi's sarcoma-associated herpesvirus interacts with origin recognition complexes at the LANA binding sequence within the terminal repeats.

Kaposi's sarcoma-associated herpesvirus (KSHV) DNA persists in latently infected cells as an episome via tethering to the host chromosomes. The latency-associated nuclear antigen (LANA) of KSHV binds to the cis-acting elements in the terminal repeat (TR) region of the genome through its carboxy terminus. Previous studies have demonstrated that LANA is important for episome maintenance and replication of the TR-containing plasmids. Here we report that LANA associates with origin recognition complexes (ORCs) when bound to its 17-bp LANA binding cognate sequence (LBS). Chromatin immunoprecipitation of multiple regions across the entire genome from two KSHV-infected cell lines, BC-3 and BCBL-1, revealed that the ORCs predominantly associated with the chromatin structure at the TR as well as two regions within the long unique region of the genome. Coimmunoprecipitation of ORCs with LANA-specific antibodies shows that ORCs can bind and form complexes with LANA in cells. This association was further supported by in vitro binding studies which showed that ORCs associate with LANA predominantly through the carboxy-terminal DNA binding region. KSHV-positive BC-3 and BCBL-1 cells arrested in G(1)/S phase showed colocalization of LANA with ORCs. Furthermore, replication of The TR-containing plasmid required both the N- and C termini of LANA in 293 and DG75 cells. Interestingly, our studies did not detect cellular ORCs associated with packaged viral DNA as an analysis of purified virions did not reveal the presence of ORCs, minichromosome maintenance proteins, or LANA.

Antigens, Viral↗
PubMed1993

Gene cluster involved in melanin biosynthesis of the filamentous fungus Alternaria alternata.

The filamentous fungus Alternaria alternata produces melanin, a black pigment, from acetate via 1,8-dihydroxynaphthalene. To isolate a fungal gene required for melanin biosynthesis, we transformed an A. alternata Brm1- (light brown) mutant with the DNA of a wild-type strain genomic library constructed by use of a cosmid carrying the hygromycin B phosphotransferase gene. When hygromycin B-resistant transformants were screened for melanin production, 1 of 1,363 transformants appeared to regain melanin production, as judged by black pigmentation of the cultured mycelia. The cosmid, named pMBR1, was recovered by packaging nuclear DNA of the melanin-producing transformant into lambda phage. The gene on pMBR1 that enables the Brm1- mutant to produce melanin was designated BRM1. In addition to the BRM1 gene, pMBR1 was found to carry two more genes involved in melanin biosynthesis. These two genes, designated ALM and BRM2, transformed A. alternata Alm- (albino) and Brm2- (brown) mutants, respectively, to the wild-type phenotype. The three genes are located within a ca. 30-kb genomic region in the order ALM-BRM1-BRM2. Analysis of the gene transcripts indicated approximate sizes of 7.2, 4.0, and 0.9 kb for ALM, BRM1, and BRM2, respectively. The BRM1 and BRM2 transcripts are generated from the same strand, but the ALM transcript is generated from the opposite strand. The three mRNA species accumulate in cultured mycelia of the wild-type strain synchronously with mycelial melanization. The essential roles of the three genes in melanin biosynthesis were confirmed by transformation-mediated gene disruption experiments.

Alternaria↗
PubMed1996

Effect of eugenol on the mutagenicity of benzo[a]pyrene and the formation of benzo[a]pyrene-DNA adducts in the lambda-lacZ-transgenic mouse.

To study the possible reduction by eugenol of the mutagenicity and genotoxicity of benzo[a]pyrene (B[a]P) in vivo, the lambda-lacZ-transgenic mouse strain 40.6 (Muta Mouse) was used. Male mice were fed a diet containing 0.4% (w/w) eugenol or a control diet for 58 days. On day 10, half of the mice received an i.p. dose of 100 mg/kg b.w. B[a]P. The lacZ mutants were recovered by packaging of DNA isolated from liver into lambda phage, and expressed in E. coli C lacZ-recA-galE- bacteria. In both control mice and mice fed the eugenol diet, B[a]P treatment resulted in a similar, significant increase in lacZ mutant frequency. Eugenol was not mutagenic by itself. By 32P-postlabelling analysis of the liver DNA using an analysis method with chromatographic conditions for B[a]P-DNA adducts, no effect of eugenol on the formation of B[a]P-DNA adducts in the lambda-lacZ-transgenic mouse was found. By 32P-postlabelling analysis using an alkenylbenzene solvent system the amount of B[a]P-DNA adducts was lower in mice fed the eugenol diet than in mice fed the control diet but the decrease was not statistically significant. However, one spot indicative of an eugenol-associated DNA adduct was detected. The present data provide no evidence for antimutagenic or antigenotoxic potential of eugenol in vivo. Furthermore, they suggest genotoxicity in vivo of eugenol per se.

Animals↗
PubMed2005

The pp24 phosphoprotein of Mason-Pfizer monkey virus contributes to viral genome packaging.

BACKGROUND: The Gag protein of Mason-Pfizer monkey virus, a betaretrovirus, contains a phosphoprotein that is cleaved into the Np24 protein and the phosphoprotein pp16/18 during virus maturation. Previous studies by Yasuda and Hunter (J. Virology. 1998. 72:4095-4103) have demonstrated that pp16/18 contains a viral late domain required for budding and that the Np24 protein plays a role during the virus life cycle since deletion of this N-terminal domain blocked virus replication. The function of the Np24 domain, however, is not known. RESULTS: Here we identify a region of basic residues (KKPKR) within the Np24 domain that is highly conserved among the phosphoproteins of various betaretroviruses. We show that this KKPKR motif is required for virus replication yet dispensable for procapsid assembly, membrane targeting, budding and release, particle maturation, or viral glycoprotein packaging. Additional experiments indicated that deletion of this motif reduced viral RNA packaging 6-8 fold and affected the transient association of Gag with nuclear pores. CONCLUSION: These results demonstrate that the Np24 domain plays an important role in RNA packaging and is in agreement with evidence that suggests that correct intracellular targeting of Gag to the nuclear compartment is an fundamental step in the retroviral life cycle.

Capsid Proteins↗