scholarly journals Diversification of giant and large eukaryotic dsDNA viruses predated the origin of modern eukaryotes

2018 ◽  
Author(s):  
Julien Guglielmini ◽  
Anthony Woo ◽  
Mart Krupovic ◽  
Patrick Forterre ◽  
Morgan Gaia
Keyword(s):  
Phylogenetic Trees ◽  
Dna Viruses ◽  
Double Stranded Dna ◽  
Virion Morphogenesis ◽  
History Of ◽  
Eukaryotic Dna ◽  
Dsdna Viruses ◽  
Virion Formation

AbstractGiant and large eukaryotic double-stranded DNA viruses from the Nucleo-Cytoplasmic Large DNA Virus (NCLDV) assemblage represent a remarkably diverse and potentially ancient component of the eukaryotic virome. However, their origin(s), evolution and potential roles in the emergence of modern eukaryotes remain a subject of intense debate. Since the characterization of the mimivirus in 2003, many big and giant viruses have been discovered at a steady pace, offering a vast material for evolutionary investigations. In parallel, phylogenetic tools are constantly being improved, offering more rigorous approaches for reconstruction of deep evolutionary history of viruses and their hosts. Here we present robust phylogenetic trees of NCLDVs, based on the 8 most conserved proteins responsible for virion morphogenesis and informational processes. Our results uncover the evolutionary relationships between different NCLDV families and support the existence of two superclades of NCLDVs, each encompassing several families. We present evidence strongly suggesting that the NCLDV core genes, which are involved in both informational processes and virion formation, were acquired vertically from a common ancestor. Among them, the largest subunits of the DNA-dependent RNA polymerase were seemingly transferred from two clades of NCLDVs to proto-eukaryotes, giving rise to two of the three eukaryotic DNA-dependent RNA polymerases. Our results strongly suggest that these transfers and the diversification of NCLDVs predated the emergence of modern eukaryotes, emphasizing the major role of viruses in the evolution of cellular domains.

scholarly journals Diversification of giant and large eukaryotic dsDNA viruses predated the origin of modern eukaryotes

2019 ◽  
Vol 116 (39) ◽  
pp. 19585-19592 ◽  
Author(s):  
Julien Guglielmini ◽  
Anthony C. Woo ◽  
Mart Krupovic ◽  
Patrick Forterre ◽  
Morgan Gaia
Keyword(s):  
Phylogenetic Trees ◽  
Dna Viruses ◽  
Double Stranded Dna ◽  
Virion Morphogenesis ◽  
Eukaryotic Dna ◽  
Dsdna Viruses ◽  
Virion Formation ◽  
Intense Debate ◽  
Core Genes

Giant and large eukaryotic double-stranded DNA viruses from the Nucleo-Cytoplasmic Large DNA Virus (NCLDV) assemblage represent a remarkably diverse and potentially ancient component of the eukaryotic virome. However, their origin(s), evolution, and potential roles in the emergence of modern eukaryotes remain subjects of intense debate. Here we present robust phylogenetic trees of NCLDVs, based on the 8 most conserved proteins responsible for virion morphogenesis and informational processes. Our results uncover the evolutionary relationships between different NCLDV families and support the existence of 2 superclades of NCLDVs, each encompassing several families. We present evidence strongly suggesting that the NCLDV core genes, which are involved in both informational processes and virion formation, were acquired vertically from a common ancestor. Among them, the largest subunits of the DNA-dependent RNA polymerase were transferred between 2 clades of NCLDVs and proto-eukaryotes, giving rise to 2 of the 3 eukaryotic DNA-dependent RNA polymerases. Our results strongly suggest that these transfers and the diversification of NCLDVs predated the emergence of modern eukaryotes, emphasizing the major role of viruses in the evolution of cellular domains.

scholarly journals Specificity of Baculovirus P6.9 Basic DNA-Binding Proteins and Critical Role of the C Terminus in Virion Formation

2010 ◽  
Vol 84 (17) ◽  
pp. 8821-8828 ◽  
Author(s):  
Manli Wang ◽  
Era Tuladhar ◽  
Shu Shen ◽  
Hualin Wang ◽  
Monique M. van Oers ◽  
...  
Keyword(s):  
Virus Assembly ◽  
Critical Role ◽  
Nucleocapsid Proteins ◽  
Double Stranded Dna ◽  
C Terminus ◽  
Sequence Elements ◽  
Eukaryotic Organisms ◽  
Dsdna Viruses ◽  
Virion Formation

ABSTRACT The majority of double-stranded DNA (dsDNA) viruses infecting eukaryotic organisms use host- or virus-expressed histones or protamine-like proteins to condense their genomes. In contrast, members of the Baculoviridae family use a protamine-like protein named P6.9. The dephosphorylated form of P6.9 binds to DNA in a non-sequence-specific manner. By using a p6.9-null mutant of Autographa californica multiple nucleopolyhedrovirus (AcMNPV), we demonstrate that P6.9 is not required for viral DNA replication but is essential for the production of infectious virus. Virion production was rescued by P6.9 homologs from a number of Alpha baculovirus species and one Gammabaculovirus species but not from the genus Betabaculovirus, comprising the granuloviruses, or by the P6.9 homolog VP15 from the unrelated white spot syndrome virus of shrimp. Mutational analyses demonstrated that AcMNPV P6.9 with a conserved 11-residue deletion of the C terminus was not capable of rescuing p6.9-null AcMNPV, while a chimeric Betabaculovirus P6.9 containing the P6.9 C-terminal region of an Alphabaculovirus strain was able to do so. This implies that the C terminus of baculovirus P6.9 contains sequence elements essential for virion formation. Such elements may possibly interact with species- or genus-specific domains of other nucleocapsid proteins during virus assembly.

scholarly journals Characterization of a Novel Thermobifida fusca Bacteriophage P318

Viruses ◽  
2019 ◽  
Vol 11 (11) ◽  
pp. 1042
Author(s):  
Cheepudom ◽  
Lin ◽  
Lee ◽  
Meng
Keyword(s):  
Plant Cell Wall ◽  
Hydrolytic Enzymes ◽  
Thermobifida Fusca ◽  
Genome Replication ◽  
Putative Orfs ◽  
Base Pairs ◽  
Double Stranded Dna ◽  
Virion Morphogenesis ◽  
Genome Information

Thermobifida fusca is of biotechnological interest due to its ability to produce an array of plant cell wall hydrolytic enzymes. Nonetheless, only one T. fusca bacteriophage with genome information has been reported to date. This study was aimed at discovering more relevant bacteriophages to expand the existing knowledge of phage diversity for this host species. With this end in view, a thermostable T. fusca bacteriophage P318, which belongs to the Siphoviridae family, was isolated and characterized. P318 has a double-stranded DNA genome of 48,045 base pairs with 3′-extended COS ends, on which 52 putative ORFs are organized into clusters responsible for the order of genome replication, virion morphogenesis, and the regulation of the lytic/lysogenic cycle. In comparison with T. fusca and the previously discovered bacteriophage P1312, P318 has a much lower G+C content in its genome except at the region encompassing ORF42, which produced a protein with unknown function. P1312 and P318 share very few similarities in their genomes except for the regions encompassing ORF42 of P318 and ORF51 of P1312 that are homologous. Thus, acquisition of ORF42 by lateral gene transfer might be an important step in the evolution of P318.

scholarly journals Structural studies on M. tuberculosis O6-methylguanine methyltransferase

2014 ◽  
Vol 70 (a1) ◽  
pp. C832-C832
Author(s):  
Menico Rizzi ◽  
Riccardo Miggiano ◽  
Samarpita Lahiri ◽  
Giuseppe Perugino ◽  
Maria Ciaramella ◽  
...  
Keyword(s):  
Excision Repair ◽  
Single Step ◽  
Double Stranded Dna ◽  
Nucleotide Excision ◽  
Enzymatic Systems ◽  
Methylguanine Methyltransferase ◽  
Mutagenic Effects ◽  
Wild Type Form

Mycobacterium tuberculosis (MTB) is an extremely well adapted human pathogen capable to survive for decades inside the hostile environment represented by the host's infected macrophages despite exposure to multiple potential DNA-damaging stresses. In order to maintain a remarkable low level of genetic diversity, MTB deploys different strategies of DNA repair, including multi-enzymatic systems, such as Nucleotide Excision Repair, and single-step repair. In particular, to counteract the mutagenic effects of DNA alkylation, MTB performs the direct alkylated-base reversal by sacrificing one molecule of a DNA-protein alkyltransferase, such as O6-methylguanine methyltransferase (OGT; orf: Rv1316c). We present here the biochemical and structural characterization of recombinant mycobacterial OGT (MtOGT) in its wild-type form along with its mutated variants mimicking the ones occurring in relevant clinical strains (i.e. MtOGT-T15S and MtOGT-R37L). Our studies reveal that MtOGT-R37L is severely impaired in its activity as consequence of its ten-fold lower affinity for modified double-stranded DNA (dsDNA) (1). Further investigations on a new structure-based panel of OGT versions, designed to explore different molecular environment at position 37, allowed us a better understanding of the functional role of the MtOGT Arg37-bearing loop during catalysis. Moreover, we solved the crystal structure of MtOGT in covalent complex with modified dsDNA that reveals an unprecedented MtOGT::DNA architecture, suggesting that the MtOGT monomer performing the catalysis needs assisting unreacted subunits during cooperative DNA binding. This work is supported by European Community FP7 program SYSTEMTB (Health-F4-2010-241587)

scholarly journals Characterization of Epidemic IncI1-Iγ Plasmids Harboring Ambler Class A and C Genes in Escherichia coli and Salmonella enterica from Animals and Humans

2015 ◽  
Vol 59 (9) ◽  
pp. 5357-5365 ◽  
Author(s):  
Hilde Smith ◽  
Alex Bossers ◽  
Frank Harders ◽  
Guanghui Wu ◽  
Neil Woodford ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Salmonella Enterica ◽  
Phylogenetic Trees ◽  
Functional Study ◽  
Content Type ◽  
Gene Associations ◽  
Genes Encoding ◽  
Marked Resistance

ABSTRACTThe aim of the study was to identify the plasmid-encoded factors contributing to the emergence and spread of epidemic IncI1-Iγ plasmids obtained fromEscherichia coliandSalmonella entericaisolates from animal and human reservoirs. For this, 251 IncI1-Iγ plasmids carrying various extended-spectrum β-lactamase (ESBL) or AmpC β-lactamase genes were compared using plasmid multilocus sequence typing (pMLST). Thirty-two of these plasmids belonging to different pMLST types were sequenced using Roche 454 and Illumina platforms. Epidemic IncI1-Iγ plasmids could be assigned to various dominant clades, whereas rarely detected plasmids clustered together as a distinct clade. Similar phylogenetic trees were obtained using only the plasmid backbone sequences, showing that the differences observed between the plasmids belonging to distinct clades resulted mainly from differences between their backbone sequences. Plasmids belonging to the various clades differed particularly in the presence/absence of genes encoding partitioning and addiction systems, which contribute to stable inheritance during cell division and plasmid maintenance. Despite this, plasmids belonging to the various phylogenetic clades also showed marked resistance gene associations, indicating the circulation of successful plasmid-gene combinations. The variation intraYandexcAgenes found in IncI1-Iγ plasmids is conserved within pMLST sequence types and plays a role in incompatibility, although functional study is needed to elucidate the role of these genes in plasmid epidemiology.

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.

Battling the Big Lie

2017 ◽  
Author(s):  
Melissa Feinberg
Keyword(s):  
Eastern Europe ◽  
Voice Of America ◽  
Radio Stations ◽  
East European ◽  
American Media ◽  
History Of ◽  
Radio Free Europe ◽  
Totalitarian Regimes

This chapter examines the characterization of Eastern Europe in the American media, concentrating on the role of East European émigrés in shaping American perceptions of their homeland. It focuses on the role of American-sponsored radio stations, such as the Voice of America and Radio Free Europe These radio stations broadcast an anticommunist perspective to Eastern Europe and played key roles in creating American knowledge about the region. The annual Crusade for Freedom, designed to raise money for RFE, sought to mobilize Americans against totalitarian regimes in Eastern Europe. In the American media, East Europeans were often referred to as “the captive peoples.” This chapter tells the history of this discourse of East European captivity and examines how it circulated back and forth across the Iron Curtain, moving from émigré publications into the American media and back into Eastern Europe.

Characterization of Marine Temperate Phage-Host Systems Isolated from Mamala Bay, Oahu, Hawaii

1998 ◽  
Vol 64 (2) ◽  
pp. 535-542 ◽  
Author(s):  
Sunny C. Jiang ◽  
Christina A. Kellogg ◽  
John H. Paul
Keyword(s):  
Water Samples ◽  
Blot Hybridization ◽  
Temperate Phage ◽  
Dot Blot ◽  
Dot Blot Hybridization ◽  
Double Stranded Dna ◽  
The Family ◽  
Marine Viruses

ABSTRACT To understand the ecological and genetic role of viruses in the marine environment, it is critical to know the infectivity of viruses and the types of interactions that occur between marine viruses and their hosts. We isolated four marine phages from turbid plaques by using four indigenous bacterial hosts obtained from concentrated water samples from Mamala Bay, Oahu, Hawaii. Two of the rod-shaped bacterial hosts were identified as Sphingomonas paucimobilis andFlavobacterium sp. All of the phage isolates were tailed phages and contained double-stranded DNA. Two of the phage isolates had morphologies typical of the family Siphoviridae, while the other two belonged to the families Myoviridae andPodoviridae. The head diameters of these viruses ranged from 47 to 70.7 nm, and the tail lengths ranged from 12 to 146 nm. The burst sizes ranged from 7.8 to 240 phage/bacterial cell, and the genome sizes, as determined by restriction digestion, ranged from 36 to 112 kb. The members of the Siphoviridae, T-φHSIC, and T-φD0, and the member of the Myoviridae, T-φD1B, were found to form lysogenic associations with their bacterial hosts, which were isolated from the same water samples. Hybridization of phage T-φHSIC probe with lysogenic host genomic DNA was observed in dot blot hybridization experiments, indicating that prophage T-φHSIC was integrated within the host genome. These phage-host systems are available for use in studies of marine lysogeny and transduction.

scholarly journals Molecular fossils reveal ancient associations of dsDNA viruses with several phyla of fungi

2020 ◽  
Vol 6 (1) ◽  
Author(s):  
Zhen Gong ◽  
Yu Zhang ◽  
Guan-Zhu Han
Keyword(s):  
Giant Virus ◽  
Virus Infections ◽  
Dsdna Virus ◽  
Dna Viruses ◽  
Molecular Fossils ◽  
Double Stranded Dna ◽  
Fungal Genomes ◽  
Nucleocytoplasmic Large Dna Viruses ◽  
Dsdna Viruses

Abstract Little is known about the infections of double-stranded DNA (dsDNA) viruses in fungi. Here, we use a paleovirological method to systematically identify the footprints of past dsDNA virus infections within the fungal genomes. We uncover two distinct groups of endogenous nucleocytoplasmic large DNA viruses (NCLDVs) in at least seven fungal phyla (accounting for about a third of known fungal phyla), revealing an unprecedented diversity of dsDNA viruses in fungi. Interestingly, one fungal dsDNA virus lineage infecting six fungal phyla is closely related to the giant virus Pithovirus, suggesting giant virus relatives might widely infect fungi. Co-speciation analyses indicate fungal NCLDVs mainly evolved through cross-species transmission. Taken together, our findings provide novel insights into the diversity and evolution of NCLDVs in fungi.

Characterization of unresectable cholangiocarcinoma patients treated with or without chemoradiation.

2015 ◽  
Vol 33 (3_suppl) ◽  
pp. 403-403
Author(s):  
Jane Elizabeth Rogers ◽  
Van Nguyen ◽  
Graciela M. Nogueras-Gonzalez ◽  
Christopher H. Crane ◽  
Prajnan Das ◽  
...  
Keyword(s):  
Progression Free Survival ◽  
Median Number ◽  
Primary Objective ◽  
First Line ◽  
Dismal Prognosis ◽  
History Of ◽  
Mixed Histology

403 Background: Curative treatment for cholangiocarcinoma (CC) is surgical resection. Unfortunately, most CC patients (pts) present with unresectable disease in which gemcitabine plus platinum (GEM-P) chemotherapy is the mainstay of treatment (tx). Advanced CC has a dismal prognosis with 5-year survival reported at 5-10 %. Data regarding chemoradiation (CRT) in pts with unresectable CC (uCC) remains limited. Methods: We retrospectively reviewed uCC pts from 1/1/2009 to 7/31/2013. Primary objective: to evaluate the percentage of pts treated with CRT and the median number of chemotherapy cycles given prior to CRT. Secondary objectives: response to first-line tx, progression free survival (PFS) with or without CRT, overall survival (OS) with or without CRT, and duration of CRT control. Inclusion criteria: uCC diagnosis, received tx, and had follow-up at our institution. Exclusion criteria: pts who received liver-directed therapy other than CRT, mixed histology tumors, and a history of other malignancies. Results: 114 pts were included with 62% having intrahepatic CC. Disease control (DC) (response + stable disease) with first-line tx was 75% with 71% receiving GEM-P +/- erlotinib first-line. 65% of pts received CRT with a median of 6 chemotherapy cycles given prior to CRT. DC after CRT was 62% with a median duration of radiation control of 6.4 mths. Median PFS and OS for all pts were 13.4 mths and 27.8 mths, respectively. Median PFS in the CRT group was 14.5 mths versus 11.4 mths in the no CRT group (p = 0.105). Median OS in the CRT cohort was 29.4 mths, while median OS without CRT was 22.4 mths (p = 0.005). Median OS and PFS after CRT for pts with DC on first-line tx were 32.0 months (95% CI = 24-44 mths) and 15.7 mths (95% CI =13.5-18.8 mths), respectively. Pts who progressed on first-line tx and received CRT had a median OS of 23.8 mths (95% CI = 7-30 months) and median PFS of 4.2 mths (95% CI = 2.3-9 mths). Conclusions: Our retrospective review reveals a significant improvement in median OS with CRT in uCC pts. Those with DC on first-line tx showed improvement in PFS and OS with CRT. Patient selection is key with the benefit being highest in pts with DC with first-line tx. Our results warrant further investigation of the role of CRT in uCC.

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