scholarly journals Diversity and Abundance of Single-Stranded DNA Viruses in Human Feces

2011 ◽  
Vol 77 (22) ◽  
pp. 8062-8070 ◽  
Author(s):  
Min-Soo Kim ◽  
Eun-Jin Park ◽  
Seong Woon Roh ◽  
Jin-Woo Bae
Keyword(s):  
Capsid Protein ◽  
Protein Sequences ◽  
Single Stranded Dna ◽  
Dna Viruses ◽  
Content Type ◽  
Double Stranded Dna ◽  
Abundance And Diversity ◽  
Ssdna Viruses ◽  
Virus Abundance ◽  
Large Contigs

ABSTRACTIn this study, we investigated the abundance and diversity of single-stranded DNA (ssDNA) viruses in fecal samples from five healthy individuals through a combination of serial filtration and CsCl gradient ultracentrifugation. Virus abundance ranged from 108to 109per gram of feces, and virus-to-bacterium ratios were much lower (less than 0.1) than those observed in aquatic environments (5 to 10). Viral DNA was extracted and randomly amplified using phi29 polymerase and analyzed through high-throughput 454 pyrosequencing. Among 400,133 sequences, an average of 86.2% viromes were previously uncharacterized in public databases. Among previously known viruses, double-stranded DNA podophages (52 to 74%), siphophages (11 to 30%), myophages (1 to 4%), and ssDNA microphages (3 to 9%) were major constituents of human fecal viromes. A phylogenetic analysis of 24 large contigs of microphages based on conserved capsid protein sequences revealed five distinct newly discovered evolutionary microphage groups that were distantly related to previously known microphages. Moreover, putative capsid protein sequences of five contigs were closely related to prophage-like sequences in the genomes of threeBacteroidesand threePrevotellastrains, suggesting thatBacteroidesandPrevotellaare the sources of infecting microphages in their hosts.

scholarly journals Distinct Circular Single-Stranded DNA Viruses Exist in Different Soil Types

2015 ◽  
Vol 81 (12) ◽  
pp. 3934-3945 ◽  
Author(s):  
Brian Reavy ◽  
Maud M. Swanson ◽  
Peter J. A. Cock ◽  
Lorna Dawson ◽  
Thomas E. Freitag ◽  
...  
Keyword(s):  
Soil Types ◽  
Metagenomic Sequencing ◽  
Single Stranded Dna ◽  
Dna Viruses ◽  
Unique Type ◽  
Content Type ◽  
Virus Particles ◽  
Intracellular Parasites ◽  
Ssdna Viruses ◽  
Virus Genomes

ABSTRACTThe potential dependence of virus populations on soil types was examined by electron microscopy, and the total abundance of virus particles in four soil types was similar to that previously observed in soil samples. The four soil types examined differed in the relative abundances of four morphological groups of viruses. Machair, a unique type of coastal soil in western Scotland and Ireland, differed from the others tested in having a higher proportion of tailed bacteriophages. The other soils examined contained predominantly spherical and thin filamentous virus particles, but the Machair soil had a more even distribution of the virus types. As the first step in looking at differences in populations in detail, virus sequences from Machair and brown earth (agricultural pasture) soils were examined by metagenomic sequencing after enriching for circular Rep-encoding single-stranded DNA (ssDNA) (CRESS-DNA) virus genomes. Sequences from the familyMicroviridae(icosahedral viruses mainly infecting bacteria) of CRESS-DNA viruses were predominant in both soils. Phylogenetic analysis ofMicroviridaemajor coat protein sequences from the Machair viruses showed that they spanned most of the diversity of the subfamilyGokushovirinae, whose members mainly infect obligate intracellular parasites. The brown earth soil had a higher proportion of sequences that matched the morphologically similar familyCircoviridaein BLAST searches. However, analysis of putative replicase proteins that were similar to those of viruses in theCircoviridaeshowed that they are a novel clade ofCircoviridae-related CRESS-DNA viruses distinct from knownCircoviridaegenera. Different soils have substantially different taxonomic biodiversities even within ssDNA viruses, which may be driven by physicochemical factors.

scholarly journals Discovery of Four Novel Circular Single-Stranded DNA Viruses in Fungus-Farming Termites

2018 ◽  
Vol 6 (17) ◽  
Author(s):  
Mason Kerr ◽  
Karyna Rosario ◽  
Christopher C. M. Baker ◽  
Mya Breitbart
Keyword(s):  
Termite Mounds ◽  
Single Stranded Dna ◽  
Dna Viruses ◽  
Content Type ◽  
The Family

ABSTRACT Here, we describe four novel circular single-stranded DNA viruses discovered in fungus-farming termites ( Odontotermes sp.). The viruses, named termite-associated circular virus 1 (TaCV-1) through TaCV-4, are most similar to members of the family Genomoviridae and were widely detected in African termite mounds.

scholarly journals Pacmanvirus, a New Giant Icosahedral Virus at the Crossroads between Asfarviridae and Faustoviruses

2017 ◽  
Vol 91 (14) ◽  
Author(s):  
Julien Andreani ◽  
Jacques Yaacoub Bou Khalil ◽  
Madhumati Sevvana ◽  
Samia Benamar ◽  
Fabrizio Di Pinto ◽  
...  
Keyword(s):  
African Swine Fever Virus ◽  
Acanthamoeba Castellanii ◽  
Genomic Analysis ◽  
African Swine Fever ◽  
Fever Virus ◽  
Dna Virus ◽  
Dna Viruses ◽  
Content Type ◽  
Double Stranded Dna ◽  
Protein Locus

ABSTRACT African swine fever virus, a double-stranded DNA virus that infects pigs, is the only known member of the Asfarviridae family. Nevertheless, during our isolation and sequencing of the complete genome of faustovirus, followed by the description of kaumoebavirus, carried out over the past 2 years, we observed the emergence of previously unknown related viruses within this group of viruses. Here we describe the isolation of pacmanvirus, a fourth member in this group, which is capable of infecting Acanthamoeba castellanii. Pacmanvirus A23 has a linear compact genome of 395,405 bp, with a 33.62% G+C content. The pacmanvirus genome harbors 465 genes, with a high coding density. An analysis of reciprocal best hits shows that 31 genes are conserved between African swine fever virus, pacmanvirus, faustovirus, and kaumoebavirus. Moreover, the major capsid protein locus of pacmanvirus appears to be different from those of kaumoebavirus and faustovirus. Overall, comparative and genomic analyses reveal the emergence of a new group or cluster of viruses encompassing African swine fever virus, faustovirus, pacmanvirus, and kaumoebavirus. IMPORTANCE Pacmanvirus is a newly discovered icosahedral double-stranded DNA virus that was isolated from an environmental sample by amoeba coculture. We describe herein its structure and replicative cycle, along with genomic analysis and genomic comparisons with previously known viruses. This virus represents the third virus, after faustovirus and kaumoebavirus, that is most closely related to classical representatives of the Asfarviridae family. These results highlight the emergence of previously unknown double-stranded DNA viruses which delineate and extend the diversity of a group around the asfarvirus members.

scholarly journals Medusavirus, a Novel Large DNA Virus Discovered from Hot Spring Water

2019 ◽  
Vol 93 (8) ◽  
Author(s):  
Genki Yoshikawa ◽  
Romain Blanc-Mathieu ◽  
Chihong Song ◽  
Yoko Kayama ◽  
Tomohiro Mochizuki ◽  
...  
Keyword(s):  
Dna Replication ◽  
Capsid Protein ◽  
Dna Polymerase ◽  
Major Capsid Protein ◽  
Hot Spring ◽  
Morphological Characteristics ◽  
Spring Water ◽  
Dna Virus ◽  
Dna Viruses ◽  
Content Type

ABSTRACT Recent discoveries of new large DNA viruses reveal high diversity in their morphologies, genetic repertoires, and replication strategies. Here, we report the novel features of medusavirus, a large DNA virus newly isolated from hot spring water in Japan. Medusavirus, with a diameter of 260 nm, shows a T=277 icosahedral capsid with unique spherical-headed spikes on its surface. It has a 381-kb genome encoding 461 putative proteins, 86 of which have their closest homologs in Acanthamoeba, whereas 279 (61%) are orphan genes. The virus lacks the genes encoding DNA topoisomerase II and RNA polymerase, showing that DNA replication takes place in the host nucleus, whereas the progeny virions are assembled in the cytoplasm. Furthermore, the medusavirus genome harbored genes for all five types of histones (H1, H2A, H2B, H3, and H4) and one DNA polymerase, which are phylogenetically placed at the root of the eukaryotic clades. In contrast, the host amoeba encoded many medusavirus homologs, including the major capsid protein. These facts strongly suggested that amoebae are indeed the most promising natural hosts of medusavirus, and that lateral gene transfers have taken place repeatedly and bidirectionally between the virus and its host since the early stage of their coevolution. Medusavirus reflects the traces of direct evolutionary interactions between the virus and eukaryotic hosts, which may be caused by sharing the DNA replication compartment and by evolutionarily long lasting virus-host relationships. Based on its unique morphological characteristics and phylogenomic relationships with other known large DNA viruses, we propose that medusavirus represents a new family, Medusaviridae. IMPORTANCE We have isolated a new nucleocytoplasmic large DNA virus (NCLDV) from hot spring water in Japan, named medusavirus. This new NCLDV is phylogenetically placed at the root of the eukaryotic clades based on the phylogenies of several key genes, including that encoding DNA polymerase, and its genome surprisingly encodes the full set of histone homologs. Furthermore, its laboratory host, Acanthamoeba castellanii, encodes many medusavirus homologs in its genome, including the major capsid protein, suggesting that the amoeba is the genuine natural host from ancient times of this newly described virus and that lateral gene transfers have repeatedly occurred between the virus and amoeba. These results suggest that medusavirus is a unique NCLDV preserving ancient footprints of evolutionary interactions with its hosts, thus providing clues to elucidate the evolution of NCLDVs, eukaryotes, and virus-host interaction. Based on the dissimilarities with other known NCLDVs, we propose that medusavirus represents a new viral family, Medusaviridae.

scholarly journals A New Putative Caulimoviridae Genus Discovered through Air Metagenomics

2018 ◽  
Vol 7 (14) ◽  
Author(s):  
Alberto Rastrojo ◽  
Andrés Núñez ◽  
Diego A. Moreno ◽  
Antonio Alcamí
Keyword(s):  
Viral Replication ◽  
Plant Pathogens ◽  
Replication Cycle ◽  
Host Genome ◽  
Dna Viruses ◽  
Content Type ◽  
Double Stranded Dna

Members of the Caulimoviridae family are important plant pathogens. These circular double-stranded DNA viruses may integrate into the host genome, although this integration is not required for the viral replication cycle.

scholarly journals Amplification of Uncultured Single-Stranded DNA Viruses from Rice Paddy Soil

2008 ◽  
Vol 74 (19) ◽  
pp. 5975-5985 ◽  
Author(s):  
Kyoung-Ho Kim ◽  
Ho-Won Chang ◽  
Young-Do Nam ◽  
Seong Woon Roh ◽  
Min-Soo Kim ◽  
...  
Keyword(s):  
Multiple Displacement Amplification ◽  
Rice Paddy ◽  
Viral Diversity ◽  
Single Stranded Dna ◽  
Dna Viruses ◽  
Amplification Method ◽  
Metagenome Sequencing ◽  
Biological Entities ◽  
Related Proteins ◽  
Ssdna Viruses

ABSTRACT Viruses are known to be the most numerous biological entities in soil; however, little is known about their diversity in this environment. In order to explore the genetic diversity of soil viruses, we isolated viruses by centrifugation and sequential filtration before performing a metagenomic investigation. We adopted multiple-displacement amplification (MDA), an isothermal whole-genome amplification method with φ29 polymerase and random hexamers, to amplify viral DNA and construct clone libraries for metagenome sequencing. By the MDA method, the diversity of both single-stranded DNA (ssDNA) viruses and double-stranded DNA viruses could be investigated at the same time. On the contrary, by eliminating the denaturing step in the MDA reaction, only ssDNA viral diversity could be explored selectively. Irrespective of the denaturing step, more than 60% of the soil metagenome sequences did not show significant hits (E-value criterion, 0.001) with previously reported viral sequences. Those hits that were considered to be significant were also distantly related to known ssDNA viruses (average amino acid similarity, approximately 34%). Phylogenetic analysis showed that replication-related proteins (which were the most frequently detected proteins) related to those of ssDNA viruses obtained from the metagenomic sequences were diverse and novel. Putative circular genome components of ssDNA viruses that are unrelated to known viruses were assembled from the metagenomic sequences. In conclusion, ssDNA viral diversity in soil is more complex than previously thought. Soil is therefore a rich pool of previously unknown ssDNA viruses.

scholarly journals The Ins and Outs of Herpesviral Capsids: Divergent Structures and Assembly Mechanisms across the Three Subfamilies

Viruses ◽  
2021 ◽  
Vol 13 (10) ◽  
pp. 1913
Author(s):  
Elizabeth B. Draganova ◽  
Jonathan Valentin ◽  
Ekaterina E. Heldwein
Keyword(s):  
Capsid Protein ◽  
Severe Disease ◽  
Human Herpesvirus ◽  
Dna Viruses ◽  
Double Stranded Dna ◽  
Cryo Electron Microscopy ◽  
Protein Functions ◽  
Attractive Therapeutic Target ◽  
Key Steps ◽  
Human Herpesviruses

Human herpesviruses, classified into three subfamilies, are double-stranded DNA viruses that establish lifelong latent infections within most of the world’s population and can cause severe disease, especially in immunocompromised people. There is no cure, and current preventative and therapeutic options are limited. Therefore, understanding the biology of these viruses is essential for finding new ways to stop them. Capsids play a central role in herpesvirus biology. They are sophisticated vehicles that shelter the pressurized double-stranded-DNA genomes while ensuring their delivery to defined cellular destinations on the way in and out of the host cell. Moreover, the importance of capsids for multiple key steps in the replication cycle makes their assembly an attractive therapeutic target. Recent cryo-electron microscopy reconstructions of capsids from all three subfamilies of human herpesviruses revealed not only conserved features but also remarkable structural differences. Furthermore, capsid assembly studies have suggested subfamily-specific roles of viral capsid protein homologs. In this review, we compare capsid structures, assembly mechanisms, and capsid protein functions across human herpesvirus subfamilies, highlighting the differences.

scholarly journals CRISPR/Cas9-Assisted Seamless Genome Editing in Lactobacillus plantarum and Its Application in N-Acetylglucosamine Production

2019 ◽  
Vol 85 (21) ◽  
Author(s):  
Ding Zhou ◽  
Zhennan Jiang ◽  
Qingxiao Pang ◽  
Yuan Zhu ◽  
Qian Wang ◽  
...  
Keyword(s):  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
Genome Editing ◽  
Lactobacillus Plantarum ◽  
Strain Engineering ◽  
Single Stranded Dna ◽  
Content Type ◽  
Recombination Efficiency ◽  
Double Stranded Dna ◽  
Exogenous Genes

ABSTRACT Lactobacillus plantarum is a potential starter and health-promoting probiotic bacterium. Effective, precise, and diverse genome editing of Lactobacillus plantarum without introducing exogenous genes or plasmids is of great importance. In this study, CRISPR/Cas9-assisted double-stranded DNA (dsDNA) and single-stranded DNA (ssDNA) recombineering was established in L. plantarum WCFS1 to seamlessly edit the genome, including gene knockouts, insertions, and point mutations. To optimize our editing method, phosphorothioate modification was used to improve the dsDNA insertion, and adenine-specific methyltransferase was used to improve the ssDNA recombination efficiency. These strategies were applied to engineer L. plantarum WCFS1 toward producing N-acetylglucosamine (GlcNAc). nagB was truncated to eliminate the reverse reaction of fructose-6-phosphate (F6P) to glucosamine 6-phosphate (GlcN-6P). Riboswitch replacement and point mutation in glmS1 were introduced to relieve feedback repression. The resulting strain produced 797.3 mg/liter GlcNAc without introducing exogenous genes or plasmids. This strategy may contribute to the available methods for precise and diverse genetic engineering in lactic acid bacteria and boost strain engineering for more applications. IMPORTANCE CRISPR/Cas9-assisted recombineering is restricted in lactic acid bacteria because of the lack of available antibiotics and vectors. In this study, a seamless genome editing method was carried out in Lactobacillus plantarum using CRISPR/Cas9-assisted double-stranded DNA (dsDNA) and single-stranded DNA (ssDNA) recombineering, and recombination efficiency was effectively improved by endogenous adenine-specific methyltransferase overexpression. L. plantarum WCFS1 produced 797.3 mg/liter N-acetylglucosamine (GlcNAc) through reinforcement of the GlcNAc pathway, without introducing exogenous genes or plasmids. This seamless editing strategy, combined with the potential exogenous GlcNAc-producing pathway, makes this strain an attractive candidate for industrial use in the future.

scholarly journals Genome Sequences of Two Single-Stranded DNA Viruses Identified in Varroa destructor

2018 ◽  
Vol 6 (9) ◽  
Author(s):  
Simona Kraberger ◽  
Gabriel A. Visnovsky ◽  
Ron F. van Toor ◽  
Maketalena F. Male ◽  
Kara Waits ◽  
...  
Keyword(s):  
New Zealand ◽  
Honey Bee ◽  
Honey Bees ◽  
Varroa Destructor ◽  
Genome Sequences ◽  
Single Stranded Dna ◽  
Dna Viruses ◽  
Content Type ◽  
Pathogenic Viruses ◽  
Parasitic Mite

ABSTRACT Varroa destructor is a ubiquitous and parasitic mite of honey bees, infecting them with pathogenic viruses having a major impact on apiculture. We identified two novel circular replication-associated protein (Rep)-encoding single-stranded (CRESS) DNA viruses from V. destructor sampled from a honey bee hive near Christchurch in New Zealand.

scholarly journals Single-Stranded DNA Uptake during Gonococcal Transformation

2016 ◽  
Vol 198 (18) ◽  
pp. 2515-2523 ◽  
Author(s):  
Christof Hepp ◽  
Heike Gangel ◽  
Katja Henseler ◽  
Niklas Günther ◽  
Berenike Maier
Keyword(s):  
Neisseria Gonorrhoeae ◽  
Outer Membrane ◽  
Transformation Process ◽  
Molecular Machine ◽  
Fluorescence Signal ◽  
Dna Uptake ◽  
Single Stranded Dna ◽  
Content Type ◽  
Fluorescent Marker ◽  
Double Stranded Dna

ABSTRACTNeisseria gonorrhoeaeis naturally competent for transformation. The first step of the transformation process is the uptake of DNA from the environment into the cell. This transport step is driven by a powerful molecular machine. Here, we addressed the question whether this machine imports single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) at similar rates. The fluorescence signal associated with the uptake of short DNA fragments labeled with a single fluorescent marker molecule was quantified. We found that ssDNA with a double-stranded DNA uptake sequence (DUS) was taken up with a similar efficiency as dsDNA. Imported ssDNA was degraded rapidly, and the thermonuclease Nuc was required for degradation. In anucdeletion background, dsDNA and ssDNA with a double-stranded DUS were imported and used as the substrates for transformation, whereas the import and transformation efficiencies of ssDNA with single-stranded DUS were below the detection limits. We conclude that the DNA uptake machine requires a double-stranded DUS for efficient DNA recognition and transports ssDNA and dsDNA with comparable efficiencies.IMPORTANCEBacterial transformation enables bacteria to exchange genetic information. It can speed up adaptive evolution and enhances the potential of DNA repair. The transport of DNA through the outer membrane is the first step of transformation in Gram-negative species. It is driven by a powerful molecular machine whose mechanism remains elusive. Here, we show forNeisseria gonorrhoeaethat the machine transports single- and double-stranded DNA at comparable rates, provided that the species-specific DNA uptake sequence is double stranded. Moreover, we found that single-stranded DNA taken up into the periplasm is rapidly degraded by the thermonuclease Nuc. We conclude that the secondary structure of transforming DNA is important for the recognition of self DNA but not for the process of transport through the outer membrane.

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