HSV-2 Transformation: A Multistep Process Mediated by Distinct Mutagenic DNA Sequences and Viral Genes Includes Activation of the Ras/MEK/MAPK Mitogenic Pathway

2001 ◽  
pp. 64-87
Author(s):  
L. Aurelian ◽  
C.C. Smith
Keyword(s):  
Dna Sequences ◽  
Viral Genes ◽  
Multistep Process

scholarly journals Analysis and Characterization of the Complete Genome of Tupaia (Tree Shrew) Herpesvirus

2001 ◽  
Vol 75 (10) ◽  
pp. 4854-4870 ◽  
Author(s):  
Udo Bahr ◽  
Gholamreza Darai
Keyword(s):  
Dna Sequences ◽  
Tree Shrew ◽  
Biological Properties ◽  
Open Reading Frames ◽  
Murine Cytomegalovirus ◽  
Unique Region ◽  
Viral Genes ◽  
Conserved Genes ◽  
Dna Strands ◽  
High Degree

ABSTRACT The tupaia herpesvirus (THV) was isolated from spontaneously degenerating tissue cultures of malignant lymphoma, lung, and spleen cell cultures of tree shrews (Tupaia spp.). The determination of the complete nucleotide sequence of the THV strain 2 genome resulted in a 195,857-bp-long, linear DNA molecule with a G+C content of 66.5%. The terminal regions of the THV genome and the loci of conserved viral genes were found to be G+C richer. Furthermore, no large repetitive DNA sequences could be identified. This is in agreement with the previous classification of THV as the prototype species of herpesvirus genome group F. The search for potential coding regions resulted in the identification of 158 open reading frames (ORFs) regularly distributed on both DNA strands. Seventy-six out of the 158 ORFs code for proteins that are significantly homologous to known herpesvirus proteins. The highest homologies found were to primate and rodent cytomegaloviruses. Biological properties, protein homologies, the arrangement of conserved viral genes, and phylogenetic analysis revealed that THV is a member of the subfamilyBetaherpesvirinae. The evolutionary lineages of THV and the cytomegaloviruses seem to have branched off from a common ancestor. In addition, it was found that the arrangements of conserved genes of THV and murine cytomegalovirus strain Smith, both of which are not able to form genomic isomers, are colinear with two different human cytomegalovirus (HCMV) strain AD169 genomic isomers that differ from each other in the orientation of the long unique region. The biological properties and the high degree of relatedness of THV to the mammalian cytomegaloviruses allow the consideration of THV as a model system for investigation of HCMV pathogenicity.

scholarly journals Reads Binning Improves the Assembly of Viral Genome Sequences From Metagenomic Samples

2021 ◽  
Vol 12 ◽  
Author(s):  
Kai Song
Keyword(s):  
Dna Sequences ◽  
Viral Genome ◽  
Metagenomic Data ◽  
Viral Sequence ◽  
Genome Sequences ◽  
Sequence Identification ◽  
Viral Genes ◽  
Eukaryotic Dna ◽  
Viral Sequences

Metagenomes can be considered as mixtures of viral, bacterial, and other eukaryotic DNA sequences. Mining viral sequences from metagenomes could shed insight into virus–host relationships and expand viral databases. Current alignment-based methods are unsuitable for identifying viral sequences from metagenome sequences because most assembled metagenomic contigs are short and possess few or no predicted genes, and most metagenomic viral genes are dissimilar to known viral genes. In this study, I developed a Markov model-based method, VirMC, to identify viral sequences from metagenomic data. VirMC uses Markov chains to model sequence signatures and construct a scoring model using a likelihood test to distinguish viral and bacterial sequences. Compared with the other two state-of-the-art viral sequence-prediction methods, VirFinder and PPR-Meta, my proposed method outperformed VirFinder and had similar performance with PPR-Meta for short contigs with length less than 400 bp. VirMC outperformed VirFinder and PPR-Meta for identifying viral sequences in contaminated metagenomic samples with eukaryotic sequences. VirMC showed better performance in assembling viral-genome sequences from metagenomic data (based on filtering potential bacterial reads). Applying VirMC to human gut metagenomes from healthy subjects and patients with type-2 diabetes (T2D) revealed that viral contigs could help classify healthy and diseased statuses. This alignment-free method complements gene-based alignment approaches and will significantly improve the precision of viral sequence identification.

The viral genome in transformed cells

1971 ◽  
Vol 177 (1046) ◽  
pp. 65-76 ◽  
Keyword(s):  
Dna Sequences ◽  
Transformed Cells ◽  
Wild Type ◽  
3T3 Cells ◽  
Viral Dna ◽  
Entire Genome ◽  
Unique Event ◽  
Viral Genes ◽  
Multiple Copies ◽  
Specific Antigens

Polyoma and SV 40-transformed cells carry multiple copies of the entire genome in their chromosomes; the viral DNA sequences appear to be covalently integrated into the host cell’s DNA but it is not known whether they are clustered in a reiterated tandem sequence or whether they are distributed singly or in clusters throughout the cell’s chromosomes. Some of the viral genes are transcribed into RNA and may code for the virus-specific antigens found in transformed cells. 3T3 cells transformed with a thermosensitive mutant of polyoma (Ts-a) can be induced to produce virus if the cells (Ts-a-3T3) are transferred from 38.5 to 31 °C. The data suggest that induction of viral multiplication involves the asynchronous occurrence of a unique event, after which DNA synthesis can continue even under non-permissive conditions. Superhelical closed circular dimers and trimers of polyoma DNA are synthesized as well as monomeric molecules. These oligomers can amount to 40 % of the total viral DNA; they are not obligatory precursors of the monomeric form, which is the only type found in mature virions. Oligomers are only infrequently observed (1 % or less) after infection of 3T3 cells with either wild type of the Ts-a mutant of polyoma. Several possible models to explain the origin of oligomers, the state of viral DNA in transformed cells and the nature of the activating event are discussed.

Merkel cell polyomavirus DNA sequences in the buffy coats of healthy blood donors

Blood ◽  
2011 ◽  
Vol 117 (26) ◽  
pp. 7099-7101 ◽  
Author(s):  
Cecilia Pancaldi ◽  
Valentina Corazzari ◽  
Stefania Maniero ◽  
Elisa Mazzoni ◽  
Manola Comar ◽  
...  
Keyword(s):  
Chronic Lymphocytic Leukemia ◽  
Dna Sequences ◽  
Blood Donors ◽  
Cell Transformation ◽  
Merkel Cell Polyomavirus ◽  
Lymphocytic Leukemia ◽  
Merkel Cell ◽  
Normal Tissues ◽  
Multistep Process ◽  
Tumor Virus

Merkel cell polyomavirus (MCPyV), a DNA tumor virus, has been found to be associated with Merkel cell carcinoma and chronic lymphocytic leukemia. MCPyV sequences have also been detected in various normal tissues in tumor-affected patients. Immunologic studies have detected MCPyV antibodies in as many as 80% of healthy blood donors. This high seroprevalence suggests that MCPyV infection is widespread in humans. In our study, buffy coats, which were examined for MCPyV DNA Tag sequences, showed a prevalence of 22%. Viral DNA load was revealed in blood samples from 10 to 100 molecules/100 000 cells. DNA sequencing confirmed that polymerase chain reaction amplicons belong to the MCPyV strain, MKL-1. To interpret the putative role of MCPyV in chronic lymphocytic leukemia, we may infer that, during a long period of viral persistence in blood cells, this DNA tumor virus may generate mutants, which are able to participate as cofactors in the multistep process of cell transformation.

Transcription factor/DNA interactions visualized by electron spectroscopic imaging

1992 ◽  
Vol 50 (1) ◽  
pp. 450-451
Author(s):  
David P. Bazett-Jones ◽  
Mark L. Brown
Keyword(s):  
Transcription Factor ◽  
Dna Sequences ◽  
Transcription Initiation ◽  
Molecular Mechanisms ◽  
Phosphorus Content ◽  
Spectroscopic Imaging ◽  
Electron Spectroscopic Imaging ◽  
Dna Backbone ◽  
Two Parameters ◽  
High Level

A multisubunit RNA polymerase enzyme is ultimately responsible for transcription initiation and elongation of RNA, but recognition of the proper start site by the enzyme is regulated by general, temporal and gene-specific trans-factors interacting at promoter and enhancer DNA sequences. To understand the molecular mechanisms which precisely regulate the transcription initiation event, it is crucial to elucidate the structure of the transcription factor/DNA complexes involved. Electron spectroscopic imaging (ESI) provides the opportunity to visualize individual DNA molecules. Enhancement of DNA contrast with ESI is accomplished by imaging with electrons that have interacted with inner shell electrons of phosphorus in the DNA backbone. Phosphorus detection at this intermediately high level of resolution (≈lnm) permits selective imaging of the DNA, to determine whether the protein factors compact, bend or wrap the DNA. Simultaneously, mass analysis and phosphorus content can be measured quantitatively, using adjacent DNA or tobacco mosaic virus (TMV) as mass and phosphorus standards. These two parameters provide stoichiometric information relating the ratios of protein:DNA content.

DNA sequence mapping in interphase and metaphase chromosomes by fluorescence in situ hybridization

1992 ◽  
Vol 50 (1) ◽  
pp. 496-497
Author(s):  
Barbara Trask ◽  
Susan Allen ◽  
Anne Bergmann ◽  
Mari Christensen ◽  
Anne Fertitta ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Dual Band ◽  
Nick Translation ◽  
Metaphase Chromosomes ◽  
Band Pass ◽  
Texas Red ◽  
Fluorescent Spot

Using fluorescence in situ hybridization (FISH), the positions of DNA sequences can be discretely marked with a fluorescent spot. The efficiency of marking DNA sequences of the size cloned in cosmids is 90-95%, and the fluorescent spots produced after FISH are ≈0.3 μm in diameter. Sites of two sequences can be distinguished using two-color FISH. Different reporter molecules, such as biotin or digoxigenin, are incorporated into DNA sequence probes by nick translation. These reporter molecules are labeled after hybridization with different fluorochromes, e.g., FITC and Texas Red. The development of dual band pass filters (Chromatechnology) allows these fluorochromes to be photographed simultaneously without registration shift.

Three-Dimensional Structure of Cloned T3 Connector Protein at 1.6nm Resolution

1990 ◽  
Vol 48 (1) ◽  
pp. 282-283
Author(s):  
José L. Carrascosa ◽  
José M. Valpuesta ◽  
Hisao Fujisawa
Keyword(s):  
Dna Sequences ◽  
Expression Vector ◽  
Three Dimensional ◽  
Deae Cellulose ◽  
Dna Packaging ◽  
Dimensional Structure ◽  
Two Dimensional ◽  
Freezing And Thawing ◽  
Three Dimensional Structure ◽  
Dimensional Reconstruction

The head to tail connector of bacteriophages plays a fundamental role in the assembly of viral heads and DNA packaging. In spite of the absence of sequence homology, the structure of connectors from different viruses (T4, Ø29, T3, P22, etc) share common morphological features, that are most clearly revealed in their three-dimensional structure. We have studied the three-dimensional reconstruction of the connector protein from phage T3 (gp 8) from tilted view of two dimensional crystals obtained from this protein after cloning and purification.DNA sequences including gene 8 from phage T3 were cloned, into Bam Hl-Eco Rl sites down stream of lambda promotor PL, in the expression vector pNT45 under the control of cI857. E R204 (pNT89) cells were incubated at 42°C for 2h, harvested and resuspended in 20 mM Tris HC1 (pH 7.4), 7mM 2 mercaptoethanol, ImM EDTA. The cells were lysed by freezing and thawing in the presence of lysozyme (lmg/ml) and ligthly sonicated. The low speed supernatant was precipitated by ammonium sulfate (60% saturated) and dissolved in the original buffer to be subjected to gel nitration through Sepharose 6B, followed by phosphocellulose colum (Pll) and DEAE cellulose colum (DE52). Purified gp8 appeared at 0.3M NaCl and formed crystals when its concentration increased above 1.5 mg/ml.

The role of DUBs in the post-translational control of cell migration

2019 ◽  
Vol 63 (5) ◽  
pp. 579-594 ◽  
Author(s):  
Guillem Lambies ◽  
Antonio García de Herreros ◽  
Víctor M. Díaz
Keyword(s):  
Cell Migration ◽  
Translational Control ◽  
Epithelial To Mesenchymal Transition ◽  
Extracellular Matrix Remodeling ◽  
Matrix Remodeling ◽  
Mesenchymal Transition ◽  
Tgfβ Receptors ◽  
Fundamental Process ◽  
Multistep Process

Abstract Cell migration is a multifactorial/multistep process that requires the concerted action of growth and transcriptional factors, motor proteins, extracellular matrix remodeling and proteases. In this review, we focus on the role of transcription factors modulating Epithelial-to-Mesenchymal Transition (EMT-TFs), a fundamental process supporting both physiological and pathological cell migration. These EMT-TFs (Snail1/2, Twist1/2 and Zeb1/2) are labile proteins which should be stabilized to initiate EMT and provide full migratory and invasive properties. We present here a family of enzymes, the deubiquitinases (DUBs) which have a crucial role in counteracting polyubiquitination and proteasomal degradation of EMT-TFs after their induction by TGFβ, inflammatory cytokines and hypoxia. We also describe the DUBs promoting the stabilization of Smads, TGFβ receptors and other key proteins involved in transduction pathways controlling EMT.

DNA methylation in satellite repeats disorders

2019 ◽  
Vol 63 (6) ◽  
pp. 757-771 ◽  
Author(s):  
Claire Francastel ◽  
Frédérique Magdinier
Keyword(s):  
Dna Methylation ◽  
Human Genome ◽  
Repetitive Dna ◽  
Dna Sequences ◽  
Satellite Repeats ◽  
Tremendous Progress ◽  
Genes Encoding ◽  
Dna Elements ◽  
Near Future

Abstract Despite the tremendous progress made in recent years in assembling the human genome, tandemly repeated DNA elements remain poorly characterized. These sequences account for the vast majority of methylated sites in the human genome and their methylated state is necessary for this repetitive DNA to function properly and to maintain genome integrity. Furthermore, recent advances highlight the emerging role of these sequences in regulating the functions of the human genome and its variability during evolution, among individuals, or in disease susceptibility. In addition, a number of inherited rare diseases are directly linked to the alteration of some of these repetitive DNA sequences, either through changes in the organization or size of the tandem repeat arrays or through mutations in genes encoding chromatin modifiers involved in the epigenetic regulation of these elements. Although largely overlooked so far in the functional annotation of the human genome, satellite elements play key roles in its architectural and topological organization. This includes functions as boundary elements delimitating functional domains or assembly of repressive nuclear compartments, with local or distal impact on gene expression. Thus, the consideration of satellite repeats organization and their associated epigenetic landmarks, including DNA methylation (DNAme), will become unavoidable in the near future to fully decipher human phenotypes and associated diseases.

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