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PubMed2004

Anything else but GAGA: a nonhistone protein complex reshapes chromatin structure.

The packaging of DNA in the cell nucleus is a major obstacle, but also a crucial means of control in processes such as DNA replication, recombination and gene transcription. Studies in recent years have revealed that dynamic changes in the basic nucleosome structure of chromatin play a key role, particularly in the activation and silencing of gene expression. It is widely assumed that these changes are often linked to equally important, but as yet poorly understood, modifications of higher-order chromatin architecture. Recent studies in the fruit-fly Drosophila melanogaster show how protein complexes that bind to 'GAGA' DNA elements can replace nucleosomes to create a local chromatin environment that facilitates a variety of site-specific regulatory responses. In this article, I will summarize recent insights into the composition and architecture of GAGA-binding protein complexes, and discuss their multifaceted role in homeotic gene regulation.

Animals↗
PubMed2006

Caspase 3 activation during herpes simplex virus 1 infection.

During herpes simplex virus 1 (HSV-1) infection, apoptosis is initiated by immediate early gene transcription and is later modulated by proteins synthesized in infected cells. We have previously shown that procaspase 3 levels are reduced during HSV-1 replication. We now demonstrate that a replication-defective HSV-1 recombinant virus which is incapable of packaging viral DNA into capsids activated caspase 3 but retained the ability to prevent the apoptotic process from killing the infected cells. This implies that HSV-1-dependent apoptosis is not merely a response to abortive infection. Maximum accumulation of the active form of caspase 3 accompanied complete HSV-1-dependent apoptosis. Additionally, caspase 7 was found to be activated during HSV-1-dependent apoptosis. Infected MCF-7 cells which ectopically express caspase 3 underwent more efficient apoptosis than their caspase 3-null parental counterparts, confirming that caspase 3 contributes to HSV-1-dependent apoptosis. However, caspase 3 reconstitution did not make the MCF-7 cells as sensitive as HEp-2 cells to HSV-1-dependent apoptosis, suggesting that other cellular factors may be involved in conferring resistance to this process. These results indicate that caspase 3 activation is a consequence of HSV-1 infection and have important implications in our understanding of the interactions of the virus with host cells.

Animals↗
PubMed2005

Chromatin organization in the mammalian nucleus.

Mammalian cells package their DNA into chromatin and arrange it in the nucleus as chromosomes. In interphase cells chromosomes are organized in a radial distribution with the most gene-dense chromosomes toward the center of the nucleus. Gene transcription, replication, and repair are influenced by the underlying chromatin architecture, which in turn is affected by the formation of chromosome territories. This arrangement in the nucleus presumably facilitates cellular functions to occur in an efficient and ordered fashion and exploring the link between transcription and nuclear organization will be an exciting area of further research.

Animals↗
PubMed2000

Use of electron microscopic and immunogold labeling techniques to determine polyomavirus recombinant VP1 capsid-like particles entry into mouse 3T6 cell nucleus.

Murine polyomavirus major structural protein VP1 could assemble into capsid-like particles when expressed in the baculovirus system. The recombinant capsid-like particles that were purified by CsCl density gradient centrifugation were capable of packaging host DNA. Electron microscopic and immunogold labeling techniques were used to study the entry of these VP1 recombinant capsid-like particles into mouse 3T6 cells. It was found that these VP1 recombinant capsid-like particles, which lack polyomavirus minor structural proteins (VP2 and VP3), use the same mechanism to enter mouse 3T6 cell cytoplasm and nucleus as that used by native polyomavirus virions.

Active Transport, Cell Nucleus↗
PubMed1997

Bacillus subtilis bacteriophage SPP1 terminase has a dual activity: it is required for the packaging initiation and represses its own synthesis.

The B. subtilis bacteriophage SPP1 terminase, encoded by genes 1 and 2, is required for the initiation of headful packaging. The DNA segment to which gene 1 product (G/P) binds includes the pacL and pacR sites and the late PL1 and PL2 promoters from which genes 1 to 7 are transcribed. When SPP1wt or SPP1sus115 (gene 6-) phages were used to infect a B. subtilis sup0 strain, the gene 1 to 7 mRNA synthesis was reduced at late times of infection. This was not observed, however, when either chloramphenicol was added 7 min after infection with SPP1wt or when SPP1sus114 (gene 1-) or SPP1sus19 (gene 2-) were used to infect B. subtilis sup0 cells. These results suggest that the terminase enzyme functions as a repressor of its own transcription. G/P and B. subtilis RNA polymerase (RP) bind to the pacL segment, which contains the PL1 and PL2 promoter region. The binding of G/P to the pacL site does not seem to exclude RP from the promoters, despite of the overlapping of their binding sites. It is likely that the terminase protein does not repress transcription by a mere steric hindrance of RP binding.

Bacillus Phages↗
PubMed2002

Mechanisms of chromatin assembly and transcription.

Fundamental mechanisms that regulate chromatin assembly and transcription have been elucidated recently using genetics and highly defined biochemical systems. Once DNA is packaged into chromatin, its function is controlled by the ordered recruitment of diverse enzymatic complexes that structurally remodel or chemically modify nucleosomes. Recent studies provide insight into the functional selectivity of chromatin-remodeling and -modifying complexes and how they act in specific combinations to regulate individual genes and cellular pathways.

Acetyltransferases↗
PubMed2000

Centromerization.

Centromere formation is a complex process that involves the packaging of DNA into a centromere-unique chromatin, chemical modification and the seeding of kinetochore and associated proteins. The early steps in this process, in which a chromosomal region is marked for centromerization (that is, to become resolutely committed to centromere formation), are unusual in that they can apparently occur in a DNA-sequence-independent manner. Current evidence indicates the involvement of epigenetic influences in these early steps. A number of epigenetic mechanisms that can affect centromere chromatin organization have been proposed. Here, the characteristics of these mechanisms and their relative roles as possible primary triggers for centromerization are discussed in the light of recent data.

Animals↗
PubMed2002

Evidence for dynamic alteration in histone gene clusters of Caenorhabditis elegans: a topoisomerase II connection?

Chromatin integrity is maintained throughout the cell cycle through repair mechanisms and intrinsically by the ordered packaging of DNA in association with histone proteins; however, aberrant rearrangements within and between chromosomes do occur. The role of the nuclear matrix protein topoisomerase II (TopoII) in generating chromosome breakpoints has been a focus of recent investigations. TopoII preferentially binds in vitro to scaffold-associated regions (SARs) and is involved in many DNA processing activities that require chromosome untangling. SARs, biochemically defined DNA elements rich in A + T, have been proposed to serve as structural boundaries for chromatin loops and to delineate functional domains. In our investigation of gene compartmentalization in a eukaryotic genome, SAR-associated nucleotide motifs from Drosophila were mapped in the regions of three histone gene clusters in an in silico analysis of the genome of Caenorhabditis elegans. Sites with similarity to the 15 bp consensus for TopoII cleavage were found predominantly in A + T enriched intergenic regions. Reiteration of sites matching the TopoII core consensus led to the identification of a novel core histone gene on chromosome IV and provided evidence for duplication and inversion in each of the three histone gene clusters. Breakpoint analysis of DNA flanking reiterated regions revealed potential sites for TopoII cleavage and a base composition phenomenon suggestive of a trigger for inversion events.

Amino Acid Sequence↗
PubMed2001

Chromatin structure and phaseolin gene regulation.

Chromatin structure, the organized packaging of DNA with histones in the nucleus, is now seen as a dynamic fabric that changes with development. Here, we use studies on the phaseolin (phas) gene that encodes a seed protein to show how chromatin structure interacts with the transcription machinery to accomplish rigorous spatial regulation of expression. In leaf and other vegetative tissues, a nucleosome is rotationally and translationally positioned over an ensemble of three phased TATA boxes, denying access to TBP. Current interest focuses on the mechanisms by which this architecture is remodeled during embryogenesis. The transcription factor PvALF is intrinsically involved, as are other non-histone proteins and abscisic acid. These concepts, and the possible modular nature of phas expression, are summarized together with speculations concerning the re-establishment of the nucleosome over the phas promoter during terminal stages of embryogenesis.

Chromatin↗
PubMed1997

Structure of a viral procapsid with molecular scaffolding.

The assembly of a macromolecular structure proceeds along an ordered morphogenetic pathway, and is accomplished by the switching of proteins between discrete conformations as they are added to the nascent assembly. Scaffolding proteins often play a catalytic role in the assembly process, rather like molecular chaperones. Although macromolecular assembly processes are fundamental to all biological systems, they have been characterized most thoroughly in viral systems, such as the icosahedral Escherichia coli bacteriophage phiX174. The phiX174 virion contains the proteins F, G, H and J. During assembly, two scaffoldingproteins B and D are required for the formation of a 108S, 360-A-diameter procapsid from pentameric precursors containing the F, G and H proteins. The procapsid contains 240 copies of protein D, forming an external scaffold, and 60 copies each of the internal scaffolding protein B, the capsid protein F, and the spike protein G. Maturation involves packaging of DNA and J proteins and loss of protein B, producing a 132S intermediate. Subsequent removal of the external scaffold yields the mature virion. Both the F and G proteins have the eight-stranded antiparallel beta-sandwich motif common to many plant and animal viruses. Here we describe the structure of a procapsid-like particle at 3.5-A resolution, showing how the scaffolding proteins coordinate assembly of the virus by interactions with the F and G proteins, and showing that the F protein undergoes conformational changes during capsid maturation.

Bacteriophage phi X 174↗
PubMed2001

Recombinant AAV vectors containing the foot and mouth disease virus 2A sequence confer efficient bicistronic gene expression in cultured cells and rat substantia nigra neurons.

Recombinant adeno-associated viruses (rAAVs) are promising vectors for gene therapy since they efficiently and stably transduce a variety of tissues of immunocompetent animals. The major disadvantage of rAAVs is their limited capacity to package foreign DNA (< or =5 kb). Often, co-expression of two or more genes from a single viral vector is desirable to achieve maximal therapeutic efficacy or to track transduced cells in vivo by suitable reporter genes. The internal ribosome entry site (IRES) sequence of encephalomyocarditis virus has been widely used to construct bicistronic viral vectors. However, the IRES is rather long and IRES-mediated translation can be relatively inefficient when compared with cap-dependent translation. As an alternative to the IRES for in vivo gene expression, we studied the 16 amino-acid long 2A peptide of foot and mouth disease virus (FMDV). The 2A peptide mediates the primary cis-'cleavage' of the FMDV polyprotein in a cascade of processing events that ultimately generate the mature FMDV proteins. We have generated several different rAAV genomes in which two coding regions are fused in-frame via the FMDV 2A sequence. We show that FMDV 2A efficiently mediates the generation of the expected cleavage products from the artificial fusion proteins in cells. Furthermore, we find that both EGFP and alpha- synuclein are expressed at substantially higher levels from 2A vectors than from the corresponding IRES-based vectors, while SOD-1 is expressed at comparable or slightly higher levels. Finally, we demonstrate for the first time, that the 2A sequence results in effective bicistronic gene expression in vivo after injection of 2A-dependent rAAVs into the rat substantia nigra. We conclude that 2A-containing rAAVs may represent an attractive alternative to IRES-dependent vectors for ex vivo and in vivo gene expression and gene therapy.

Animals↗
PubMed2000

Site-specific DNA binding and bending by the Borrelia burgdorferi Hbb protein.

The Borrelia burgdorferi Hbb protein shows sequence similarity to members of the Escherichia coli HU/integration host factor (IHF) family of DNA accessory factors. We have overexpressed the hbb gene product in E. coli and purified the protein to near homogeneity. Biochemical analyses have revealed that Hbb has unique properties and is neither a strict HU nor IHF analogue. Hbb was found to bind specifically to a site in the putative origin of DNA replication between dnaA and dnaN. DNA footprinting studies have shown that this site is unrelated to the consensus sequence recognized by IHF proteins. Hbb induces a dramatic bend (> 126 degrees ) at this site and was also shown to restrain negative supercoils efficiently upon DNA binding. These features of the protein suggest that Hbb may act as a DNA accessory factor that facilitates the assembly of higher order protein-DNA complexes, such as those involved in DNA replication, transcription, recombination, packaging and perhaps other DNA metabolic processes unique to Borrelia.

Bacterial Proteins↗
PubMed2003

Delivery of matrix metalloproteinase-1 attenuates established liver fibrosis in the rat.

BACKGROUND & AIMS: During hepatic fibrogenesis, the hepatic extracellular matrix changes to fibrillar collagens types I and III, and cirrhosis is believed to produce an irreversible scar. In this study, we investigated whether gene delivery of human matrix metalloproteinase-1, which degrades collagens types I and type III, would attenuate established hepatic fibrosis in the rat, induced by either thioacetamide or bile duct ligation. METHODS: Hepatic fibrosis induced by thioacetamide for 7 weeks was persistent for at least 2 months, even after discontinuation of the treatment. The rats were infected once with a recombinant adenovirus, Ad5MMP-1, into which human pro-human matrix metalloproteinase-1 complementary DNA was packaged, or with a control adenovirus, Ad5LacZ. RESULTS: In Ad5MMP-1-infected, but not in Ad5LacZ-infected, rats, the fibrosis was dramatically attenuated at 2 weeks after the infection. It is interesting to note that the number of activated hepatic stellate cells was also decreased in Ad5MMP-1-infected rats. Moreover, disorganization of the hepatic trabecula, heterogeneity in the size of hepatocytes, and increased dried liver weight were observed only in Ad5MMP-1-treated rats, suggesting that human matrix metalloproteinase-1 stimulated hepatocyte proliferation, which was confirmed by bromodeoxyuridine staining. After 4 weeks, the proliferative effect of human matrix metalloproteinase-1 almost disappeared, but the hepatic fibrosis remained attenuated, whereas the fibrosis in Ad5LacZ-treated rats persisted. Furthermore, the administration of Ad5MMP-1, but not Ad5LacZ, decreased type I collagen and generated a small collagen fragment in hepatic fibrosis induced by bile duct ligation. CONCLUSIONS: Our findings show that transient human matrix metalloproteinase-1 overexpression in the liver effectively attenuates established fibrosis and induces hepatocyte proliferation.

Adenoviridae↗
PubMed2005

Effect of condensate formation on long-distance radical cation migration in DNA.

Long-distance radical cation transport was studied in DNA condensates. Linearized pUC19 plasmid was ligated to an oligomer containing a covalently linked anthraquinone group and six regularly spaced GG steps, which serve as traps for the migrating radical cation. Treatment of the linear, ligated plasmid with spermidine results in formation of condensates that were detected by light scattering and observed by transmission electron microscopy. Irradiation of the anthraquinone group in the condensate causes long-distance charge migration, which is detected by reaction at the remote guanines. The efficiency of charge migration in the condensate is significantly less than it is for the corresponding oligomer in solution. This result is attributed to a lower mobility for the migrating radical cation in the condensate, which is caused by inhibited formation of charge-transfer-effective states.

Anthraquinones↗
PubMed1985

Adenine ribo- and deoxyribonucleotide metabolism in human erythrocytes, B- and T-lymphocyte cell lines, and monocyte-macrophages.

Ordinarily packaged in DNA, adenine deoxyribonucleotides are preferentially concentrated in erythrocyte and lymphocyte cytosol in adenosine deaminase (adenosine aminohydrolase, EC 3.5.4.4) deficiency. A spectrum of cytosol enzyme activities are defined in terms of reaction velocities, K0.5s, and nucleotide partition after incubation with ribo- and deoxyribonucleotides. AMP and dAMP were dephosphorylated, but only AMP was deaminated in vitro. Although nucleotidase activity is much stronger in lymphocytes, AMP deaminase was the dominant degradative reaction in all erythrocyte and lymphocyte lysates under the conditions specified. For most cytosolic enzymes, ribonucleotides were preferred cofactors, implying that dADP and dATP often may be bystanders at metabolic events. The adenylate kinase-mediated partition of approximately equimolar ribo- and deoxyribonucleotide substrates yielded a very large preponderance of AMP in the monophosphate compartment, the monophosphates alone being directly vulnerable to degradative loss. The adenylate kinase(s) of lymphocytes differed strikingly from those of erythrocytes in reaction velocities with nucleotide cofactors, K0.5s, and in susceptibility to substrate inhibition.

AMP Deaminase↗
PubMed1996

Structural states of the nucleosome.

The nucleosome is the fundamental component of the eukaryotic chromosome, participating in the packaging of DNA and in the regulation of gene expression. Its numerous interactions imply a structural dynamism. Previous biophysical studies under limited sets of conditions have not been able to reconcile structural differences and transitions observed. We have determined a series of nucleosome conformations over a >10,000-fold range in salt concentration using a combination of biochemical methods, spectroscopic electron microscopy, and three-dimensional reconstruction techniques for randomly oriented single particles. This study indicates several ionic strength-dependent nucleosome conformations and also reconciles the differences between currently existing divergent models for the nucleosome. At low ionic environments, the particle appears highly elongated, becoming more compact and prolate ellipsoidal as ionic strength is increased to 10 mm NaCl. At 30 mM NaCl, the particle exhibits a spheroidal conformation. As ionic strength is increased to 150 mM NaCl, the nucleosome conformation changes and becomes oblate. Above 450 mM NaCl, the structure becomes highly elongated again. The result of this study is a unifying concept in which the three-dimensional structure of the nucleosome is inferred to be dynamic in response to ionic interactions and in accord with biochemical and genetic studies.

Animals↗