scholarly journals Efficient linear dsDNA tagging using deoxyuridine excision

ChemBioChem ◽  
2021 ◽  
Author(s):  
Eric J. Strobel
Keyword(s):  
Linear Dsdna

scholarly journals A Novel Genus of Actinobacterial Tectiviridae

Viruses ◽  
2019 ◽  
Vol 11 (12) ◽  
pp. 1134 ◽  
Author(s):  
Steven M. Caruso ◽  
Tagide N. deCarvalho ◽  
Anthony Huynh ◽  
George Morcos ◽  
Nansen Kuo ◽  
...  
Keyword(s):  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Genome Structure ◽  
Dna Delivery ◽  
Transmission Electron ◽  
Viral Particles ◽  
Ancient Lineage ◽  
Linear Dsdna ◽  
Streptomyces Scabiei ◽  
Potato Crops

Streptomyces phages WheeHeim and Forthebois are two novel members of the Tectiviridae family. These phages were isolated on cultures of the plant pathogen Streptomyces scabiei, known for its worldwide economic impact on potato crops. Transmission electron microscopy showed viral particles with double-layered icosahedral capsids, and frequent instances of protruding nanotubes harboring a collar-like structure. Mass-spectrometry confirmed the presence of lipids in the virion, and serial purification of colonies from turbid plaques and immunity testing revealed that both phages are temperate. Streptomyces phages WheeHeim and Forthebois have linear dsDNA chromosomes (18,266 bp and 18,251 bp long, respectively) with the characteristic two-segment architecture of the Tectiviridae. Both genomes encode homologs of the canonical tectiviral proteins (major capsid protein, packaging ATPase and DNA polymerase), as well as PRD1-type virion-associated transglycosylase and membrane DNA delivery proteins. Comparative genomics and phylogenetic analyses firmly establish that these two phages, together with Rhodococcus phage Toil, form a new genus within the Tectiviridae, which we have tentatively named Deltatectivirus. The identification of a cohesive clade of Actinobacteria-infecting tectiviruses with conserved genome structure but with scant sequence similarity to members of other tectiviral genera confirms that the Tectiviridae are an ancient lineage infecting a broad range of bacterial hosts.

scholarly journals Adintoviruses: A Proposed Animal-Tropic Family of Midsize Eukaryotic Linear dsDNA (MELD) Viruses

2020 ◽  
Author(s):  
Gabriel J Starrett ◽  
Michael J Tisza ◽  
Nicole L Welch ◽  
Anna K Belford ◽  
Alberto Peretti ◽  
...  
Keyword(s):  
Genome Packaging ◽  
Metagenomic Sequence ◽  
Dna Viruses ◽  
Diverse Range ◽  
Integrase Gene ◽  
Data Mining Approach ◽  
Double Stranded Dna ◽  
Wide Range ◽  
Linear Dsdna ◽  
Dsdna Viruses

Abstract Polintons (also known as Mavericks) were initially identified as a widespread class of eukaryotic transposons named for their hallmark type B DNA polymerase and retrovirus-like integrase genes. It has since been recognized that many polintons encode possible capsid proteins and viral genome-packaging ATPases similar to those of a diverse range of double-stranded DNA (dsDNA) viruses. This supports the inference that at least some polintons are actually viruses capable of cell-to-cell spread. At present, there are no polinton-associated capsid protein genes annotated in public sequence databases. To rectify this deficiency, we used a data-mining approach to investigate the distribution and gene content of polinton-like elements and related DNA viruses in animal genomic and metagenomic sequence datasets. The results define a discrete family-like clade of viruses with two genus-level divisions. We propose the family name Adintoviridae, connoting similarities to adenovirus virion proteins and the presence of a retrovirus-like integrase gene. Although adintovirus-class PolB sequences were detected in datasets for fungi and various unicellular eukaryotes, sequences resembling adintovirus virion proteins and accessory genes appear to be restricted to animals. Degraded adintovirus sequences are endogenized into the germlines of a wide range of animals, including humans.

A one-pot functionalization strategy for immobilizing proteins onto linear dsDNA scaffolds

2009 ◽  
Vol 20 (23) ◽  
pp. 235101 ◽  
Author(s):  
Lorenzo Berti ◽  
Igor L Medintz ◽  
Andrea Alessandrini ◽  
Paolo Facci
Keyword(s):  
One Pot ◽  
Linear Dsdna

scholarly journals A virus of hyperthermophilic archaea with a unique architecture among DNA viruses

2016 ◽  
Vol 113 (9) ◽  
pp. 2478-2483 ◽  
Author(s):  
Elena Ilka Rensen ◽  
Tomohiro Mochizuki ◽  
Emmanuelle Quemin ◽  
Stefan Schouten ◽  
Mart Krupovic ◽  
...  
Keyword(s):  
Ebola Virus ◽  
Inner Core ◽  
Genetic Material ◽  
Marburg Virus ◽  
Hyperthermophilic Archaea ◽  
Virion Protein ◽  
Host Cell Membrane ◽  
Dna Viruses ◽  
The Family ◽  
Linear Dsdna

Viruses package their genetic material in diverse ways. Most known strategies include encapsulation of nucleic acids into spherical or filamentous virions with icosahedral or helical symmetry, respectively. Filamentous viruses with dsDNA genomes are currently associated exclusively with Archaea. Here, we describe a filamentous hyperthermophilic archaeal virus,Pyrobaculumfilamentous virus 1 (PFV1), with a type of virion organization not previously observed in DNA viruses. The PFV1 virion, 400 ± 20 × 32 ± 3 nm, contains an envelope and an inner core consisting of two structural units: a rod-shaped helical nucleocapsid formed of two 14-kDa major virion proteins and a nucleocapsid-encompassing protein sheath composed of a single major virion protein of 18 kDa. The virion organization of PFV1 is superficially similar to that of negative-sense RNA viruses of the familyFiloviridae, including Ebola virus and Marburg virus. The linear dsDNA of PFV1 carries 17,714 bp, including 60-bp-long terminal inverted repeats, and contains 39 predicted ORFs, most of which do not show similarities to sequences in public databases. PFV1 is a lytic virus that completely disrupts the host cell membrane at the end of the infection cycle.

scholarly journals ICTV Virus Taxonomy Profile: Ovaliviridae

2020 ◽  
Author(s):  
Li Huang ◽  
Haina Wang ◽  
Keyword(s):  
Viral Genome ◽  
International Committee ◽  
Virus Taxonomy ◽  
Enveloped Viruses ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Virus Progeny ◽  
Linear Dsdna ◽  
Infected Cells

Ovaliviridae is a family of enveloped viruses with a linear dsDNA genome. The virions are ellipsoidal, and contain a multi-layered spool-like capsid. The viral genome is presumably replicated through protein priming by a putative DNA polymerase encoded by the virus. Progeny virions are released through hexagonal openings resulting from the rupture of virus-associated pyramids formed on the surface of infected cells. The only known host is a hyperthermophilic archaeon of the genus Sulfolobus . This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Ovaliviridae, which is available at ictv.global/report/ovaliviridae.

scholarly journals CRISPR-Cas12a–assisted PCR tagging of mammalian genes

2020 ◽  
Vol 219 (6) ◽  
Author(s):  
Julia Fueller ◽  
Konrad Herbst ◽  
Matthias Meurer ◽  
Krisztina Gubicza ◽  
Bahtiyar Kurtulmus ◽  
...  
Keyword(s):  
Tissue Culture ◽  
Fluorescent Protein ◽  
Mammalian Tissue ◽  
Target Enrichment ◽  
Culture Cells ◽  
Endogenous Expression ◽  
Tissue Culture Cells ◽  
Potential Sources ◽  
Linear Dsdna ◽  
Mammalian Genes

Here we describe a time-efficient strategy for endogenous C-terminal gene tagging in mammalian tissue culture cells. An online platform is used to design two long gene-specific oligonucleotides for PCR with generic template cassettes to create linear dsDNA donors, termed PCR cassettes. PCR cassettes encode the tag (e.g., GFP), a Cas12a CRISPR RNA for cleavage of the target locus, and short homology arms for directed integration via homologous recombination. The integrated tag is coupled to a generic terminator shielding the tagged gene from the co-inserted auxiliary sequences. Co-transfection of PCR cassettes with a Cas12a-encoding plasmid leads to robust endogenous expression of tagged genes, with tagging efficiency of up to 20% without selection, and up to 60% when selection markers are used. We used target-enrichment sequencing to investigate all potential sources of artifacts. Our work outlines a quick strategy particularly suitable for exploratory studies using endogenous expression of fluorescent protein–tagged genes.

scholarly journals Halobacterium salinarum virus ChaoS9, a Novel Halovirus Related to PhiH1 and PhiCh1

Genes ◽  
2019 ◽  
Vol 10 (3) ◽  
pp. 194 ◽  
Author(s):  
Mike Dyall-Smith ◽  
Peter Palm ◽  
Gerhard Wanner ◽  
Angela Witte ◽  
Dieter Oesterhelt ◽  
...  
Keyword(s):  
Unit Length ◽  
Halobacterium Salinarum ◽  
Tail Fiber ◽  
Homogeneous Population ◽  
Head Assembly ◽  
Linear Dsdna ◽  
Natrialba Magadii ◽  
The Right ◽  
Haloarcula Hispanica ◽  
Assembly Proteins

The unexpected lysis of a large culture of Halobacterium salinarum strain S9 was found to be caused by a novel myovirus, designated ChaoS9. Virus purification from the culture lysate revealed a homogeneous population of caudovirus-like particles. The viral genome is linear, dsDNA that is partially redundant and circularly permuted, has a unit length of 55,145 nt, a G + C% of 65.3, and has 85 predicted coding sequences (CDS) and one tRNA (Arg) gene. The left arm of the genome (0–28 kbp) encodes proteins similar in sequence to those from known caudoviruses and was most similar to myohaloviruses phiCh1 (host: Natrialba magadii) and phiH1 (host: Hbt. salinarum). It carries a tail-fiber gene module similar to the invertible modules present in phiH1 and phiCh1. However, while the tail genes of ChaoS9 were similar to those of phiCh1 and phiH1, the Mcp of ChaoS9 was most similar (36% aa identity) to that of Haloarcula hispanica tailed virus 1 (HHTV-1). Provirus elements related to ChaoS9 showed most similarity to tail/assembly proteins but varied in their similarity with head/assembly proteins. The right arm (29–55 kbp) of ChaoS9 encoded proteins involved in DNA replication (ParA, RepH, and Orc1) but the other proteins showed little similarity to those from phiH1, phiCh1, or provirus elements, and most of them could not be assigned a function. ChaoS9 is probably best classified within the genus Myohalovirus, as it shares many characteristics with phiH1 (and phiCh1), including many similar proteins. However, the head/assembly gene region appears to have undergone a recombination event, and the inferred proteins are different to those of phiH1 and phiCh1, including the major capsid protein. This makes the taxonomic classification of ChaoS9 more ambiguous. We also report a revised genome sequence and annotation of Natrialba virus phiCh1.

scholarly journals Characterization of strand exchange activity of yeast Rad51 protein.

1997 ◽  
Vol 17 (9) ◽  
pp. 5359-5368 ◽  
Author(s):  
E Namsaraev ◽  
P Berg
Keyword(s):  
Genetic Recombination ◽  
Strand Exchange ◽  
Dna Double Strand Breaks ◽  
Strand Breaks ◽  
Ssdna Binding ◽  
Double Stranded Dna ◽  
Ssdna Binding Protein ◽  
Linear Dsdna ◽  
Circular Ssdna

The Saccharomyces cerevisiae RAD51 gene product takes part in genetic recombination and repair of DNA double strand breaks. Rad51, like Escherichia coli RecA, catalyzes strand exchange between homologous circular single-stranded DNA (ssDNA) and linear double-stranded DNA (dsDNA) in the presence of ATP and ssDNA-binding protein. The formation of joint molecules between circular ssDNA and linear dsDNA is initiated at either the 5' or the 3' overhanging end of the complementary strand; joint molecules are formed only if the length of the overhanging end is more than 1 nucleotide. Linear dsDNAs with recessed complementary or blunt ends are not utilized. The polarity of strand exchange depends upon which end is used to initiate the formation of joint molecules. Joint molecules formed via the 5' end are processed by branch migration in the 3'-to-5' direction with respect to ssDNA, and joint molecules formed with a 3' end are processed in the opposite direction.

scholarly journals Uncatalyzed assembly of spherical particles from SV40 VP1 pentamers and linear dsDNA incorporates both low and high cooperativity elements

Virology ◽  
2010 ◽  
Vol 397 (1) ◽  
pp. 199-204 ◽  
Author(s):  
Santanu Mukherjee ◽  
Stanislav Kler ◽  
Ariella Oppenheim ◽  
Adam Zlotnick
Keyword(s):  
Spherical Particles ◽  
Linear Dsdna

scholarly journals The mitochondrial genome of the pathogenic yeast Candida subhashii: GC-rich linear DNA with a protein covalently attached to the 5′ termini

Microbiology ◽  
2010 ◽  
Vol 156 (7) ◽  
pp. 2153-2163 ◽  
Author(s):  
Dominika Fricova ◽  
Matus Valach ◽  
Zoltan Farkas ◽  
Ilona Pfeiffer ◽  
Judit Kucsera ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Large Scale ◽  
Dna Polymerases ◽  
Specific Primers ◽  
Pathogenic Yeast ◽  
Unknown Protein ◽  
The Family ◽  
Linear Dsdna ◽  
Linear Molecules ◽  
Terminal Proteins

As a part of our initiative aimed at a large-scale comparative analysis of fungal mitochondrial genomes, we determined the complete DNA sequence of the mitochondrial genome of the yeast Candida subhashii and found that it exhibits a number of peculiar features. First, the mitochondrial genome is represented by linear dsDNA molecules of uniform length (29 795 bp), with an unusually high content of guanine and cytosine residues (52.7 %). Second, the coding sequences lack introns; thus, the genome has a relatively compact organization. Third, the termini of the linear molecules consist of long inverted repeats and seem to contain a protein covalently bound to terminal nucleotides at the 5′ ends. This architecture resembles the telomeres in a number of linear viral and plasmid DNA genomes classified as invertrons, in which the terminal proteins serve as specific primers for the initiation of DNA synthesis. Finally, although the mitochondrial genome of C. subhashii contains essentially the same set of genes as other closely related pathogenic Candida species, we identified additional ORFs encoding two homologues of the family B protein-priming DNA polymerases and an unknown protein. The terminal structures and the genes for DNA polymerases are reminiscent of linear mitochondrial plasmids, indicating that this genome architecture might have emerged from fortuitous recombination between an ancestral, presumably circular, mitochondrial genome and an invertron-like element.

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