Encodes archaeal viruses. Medical search. Frequent questions

All archaeal and many bacterial genomes contain Clustered Regularly Interspaced Short Palindrome Repeats (CRISPR) and variable arrays of the CRISPR-associated ( cas ) genes that have been previously implicated in a novel form of DNA repair on the basis of comparative analysis of their protein product sequences. (biomedcentral.com)
The functioning of this system seems to involve integration of fragments of foreign genes into archaeal and bacterial chromosomes yielding heritable immunity to the respective agents. (biomedcentral.com)
Finally, a locus of genes is identified in the host cell, encoding proteins essential for viral infection, that are likely components of the pili structure recognized by STIV. (montana.edu)
Gene content and phylogenetic analyses illuminated a robust connection between pTN2-like plasmids and Pyrococcus abyssi virus 1 (PAV1), with roughly half of the viral genome being composed of genes that have homologues in plasmids. (pasteur.fr)
Notably, although abundant in archaeal genomes, to our knowledge, TA and hfq-like genes have not been previously found in archaeal plasmids or viruses. (pasteur.fr)
Carrying and disseminating auxiliary metabolic genes (AMGs) associated with the degradation of polysaccharides, sulfate reduction, denitrification, and organic phosphoester hydrolysis, as well as the lysis of crucial functional microbes that govern biogeochemical cycles were two major ways by which viruses could regulate AS functions. (biomedcentral.com)
It was worth noting that our study revealed a high abundance of antibiotic resistance genes (ARGs) in viral genomes, suggesting that viruses were key reservoirs of ARGs in AS systems. (biomedcentral.com)
In addition, viruses have been shown to regulate the metabolic processes of ecosystems by encoding auxiliary metabolic genes (AMGs) [ 11 ]. (biomedcentral.com)
Viruses are also considered to be potential reservoirs of antibiotic resistance genes (ARGs) and the delivery agents for horizontal gene transfer (HGT) of ARGs in the environment [ 7 , 12 ]. (biomedcentral.com)
Nuclear antigens encoded by VIRAL GENES found in HUMAN HERPESVIRUS 4. (lookformedical.com)
The recently reported phage genomes range up to 735 kb in length and encode a diversity of genes involved in transcription and translation, as well as genes that may augment host metabolism 2 . (nature.com)
In some mtDNAs (e.g., nematodes and annelids), all genes are transcribed in the same direction, whereas, in others, both strands encode genes. (biomedcentral.com)
Typical triploblastic animal mtDNAs contain genes that encode the large and small subunit ribosomal RNAs, 22 transfer RNAs (tRNAs), and 13 proteins that are all components of the oxidative phosphorylation process: ATPase subunits 6 and 8 (ATP6 and 8), cytochrome b (Cyt b), cytochrome c oxidase subunits 1-3 (Cox1-3) and NADH dehydrogenase subunits 1-6 and 4L (ND1-6 and 4L). (biomedcentral.com)
In that alien world, researchers have now found large DNA molecules that aren't quite viruses, which are DNA or RNA wrapped in proteins, but that seem to have infected archaea and acquired along the way a slew of genes from their archaeal hosts. (berkeley.edu)
Transfer of photosynthesis genes to and from Prochlorococcus viruses. (academicinfluence.com)
Aziz, Breitbart, and Edwards examined some 10 million genes from 2137 sequenced genomes (47 archaeal, 725 bacterial, 29 eukaryotic and 1336 viral) plus 187 metagenomes, in search of. (asmblog.org)
The research group from Aarhus - led by Associate Professor Ditlev E. Brodersen - has discovered how a part of CRISPR-Cas that is responsible for incorporating foreign, viral DNA into the microorganism's own genome has originated from another, very common type of genes in bacteria and archaea that surprisingly encode toxins. (azolifesciences.com)
Abundance and distribution of archaeal Group I (MCGI) genes in the coastal Arctic and the ratio archaeal 16S rDNA gene abundance in the Atlantic (D), and ratio high-ammonia focus 0.7) in the amount of OTUs attained by cloning with the HAC and the LAC primers seeing that indicated by the rarefaction curves shown in CA-074 Methyl Ester novel inhibtior Fig. S7. (healthweblognews.info)

It is unlike any other known virus infecting the archaea with a single stranded DNA genome and an external lipid envelope and is classified in the family Pleolipoviridae, genus Alphapleolipovirus, species Halorubrum virus HRPV1. (wikipedia.org)
It may be organised to form a shell around the genome as is the case in other viruses but this is not yet known. (wikipedia.org)
citation needed] Pietila, M, Laurinavicius S, Sund, J, Roine E & Bamford D (2009) The single-stranded DNA genome of novel archaeal virus Halorubrum pleomorphic virus 1 Is enclosed in the envelope decorated with glycoprotein spikes. (wikipedia.org)
Genome condensation and packaging are essential processes in the life cycle of viruses. (mdpi.com)
In addition, a revised genome annotation of SIRV2 (Sulfolobus islandicus rod-shaped virus 2) is presented. (pasteur.fr)
One assembled sequence of 5,662 nucleotides, believed to be a complete viral genome, encodes a single open reading frame containing a RdRp and a putative capsid protein similar to that of the positive-strand RNA containing nodaviruses, tetraviruses, and birnaviruses. (virology.ws)
The virus capsid serves multiple biological functions including: to protect the viral genome during transit between host cells, and to facilitate attachment and entry of the viral genome to a new host cell. (montana.edu)
Characterization of this new virus was conducted, including genome sequencing and determination of the protein identity for the capsid fibers. (montana.edu)
This study reveals a new mechanism for the fluid gain of beneficial mutations in genetic regions undergoing active recombination in viruses and illustrates the value of long read sequencing technologies for investigating complex genome dynamics in diverse biological systems. (elifesciences.org)
Thus, for genome replication these viruses necessarily depend on helper viruses which can belong to different families. (hal.science)
Just as our immune system remembers the pathogens we have been exposed to earlier in life, CRISPR-Cas provides microorganisms with an ability to respond quickly to viruses they have previously encountered by storing a small amount of the viral DNA in their own genome. (azolifesciences.com)

Global distribution of nearly identical phage-encoded DNA sequences. (academicinfluence.com)
Here the phage-encoded holin proteins are said to "permeabilize" the E. coli membrane, thus allowing. (asmblog.org)
These small, phage-encoded proteins time the length of lytic infections of some phages. (asmblog.org)

Archaeal viruses, especially viruses that infect hyperthermophilic archaea of the phylum Crenarchaeota, constitute one of the least understood parts of the virosphere. (pasteur.fr)
An RNA virus that infects Archaea? (virology.ws)
While the majority of the known viruses infect bacteria and eukaryotes, there are only about 50 known viruses of the Archaea , and these all have DNA genomes. (virology.ws)
80°C) springs in Yellowstone National Park were examined for the presence of archaeal RNA viruses because these bodies of water contain mainly Archaea . (virology.ws)
However whether or not the hosts of these viruses are Archaea or Bacteria cannot be determined by these metagenomic analyses. (virology.ws)
2 thoughts on "An RNA virus that infects Archaea? (virology.ws)
An interesting alternative way of looking for RNA viruses would be to do dsRNA isolation on concentrated bacteria/archaea: this is a VERY under-appreciated way of very quickly enriching for (+) and dsRNA viruses. (virology.ws)
iPHoP: A Matchmaker for Phages and their Hosts Building on existing virus-host prediction approaches, a new tool combines and evaluates multiple predictions to reliably match viruses with their archaea and bacteria hosts. (doe.gov)
It's a realm where bacteria, bacteria-like organisms called archaea and fungi mingle with viruses and other non-living bits of DNA or DNA - all living with, in or on one another. (berkeley.edu)

In contrast, the means of handling and copying DNA vary quite a bit, with, for example, the major bacterial DNA processing enzymes lacking archaeal/eukaryotic homologs . (3quarksdaily.com)
Like eukaryotic and archaeal viruses, which coopt the host's cellular pathways for their replication, bacteriophages have evolved strategies to alter the metabolism of their bacterial host. (uni-hannover.de)

Sulfolobus turreted icosahedral virus (STIV) is well characterized for an archaeal virus. (montana.edu)
One of these HDPs has been identified in human 11-hydroxysteroid dehydrogenase-1 β-like, the other represents the first HDP from an archaeal protein, the transcription factor Stf76 encoded by the hybrid plasmid-virus pSSVx from Sulfolobus islandicus. (unina.it)
TFS4 is encoded by the Sulfolobus host and is expressed in response to infection with the Sulfolobus Turreted Icosahedral Virus (STIV). (lon.ac.uk)
But even though Sulfolobus has chosen a very unattractive place to live, it still encounters resistance, not the least from small, rod-shaped DNA viruses that constantly poke holes in the cells and shoot their foreign DNA into them, causing Sulfolobus to explode in a wealth of new virus particles. (azolifesciences.com)
But in the constantly escalating battle between life and death, the virus has developed a countermeasure: It has managed to cope by producing a small weapon, an anti-CRISPR protein that, like upsetting the applecart, blocks the CRISPR-Cas response in Sulfolobus. (azolifesciences.com)

At least 64% of Omnitrophota genomes encode gene clusters typical of bacterial symbionts, suggesting host-associated lifestyles. (bigelow.org)

Future work is needed to determine whether phage-associated PmoC has similar functions to additional copies of PmoC encoded in bacterial genomes, thus contributing to growth on methane. (nature.com)

Gene content analysis revealed that thermococcal plasmids encode Hfq-like proteins and toxin-antitoxin (TA) systems of two different families, VapBC and RelBE. (pasteur.fr)
Any of the processes by which cytoplasmic factors influence the differential control of gene action in viruses. (lookformedical.com)
We performed experimental evolution with vaccinia virus populations harboring a SNV in a gene actively undergoing copy number amplification. (elifesciences.org)
In order to expand our understanding of how recombination might influence virus variation during the course of adaptation, we focused on large DNA viruses, in which rapidly evolving populations can simultaneously harbor both adaptive gene copy number variation and beneficial single nucleotide variants (SNVs) at the same locus. (elifesciences.org)
Of manually curated genomes, 22 (18 are complete), ranging from 159 kilobase (kb) to 527 kb in length, were found to encode the pmoC gene, an enzymatically critical subunit of the particulate methane monooxygenase, the predominant methane oxidation catalyst in nature. (nature.com)
Bacteriophages (phages), viruses that infect and replicate within bacteria, are important in both natural and human microbiomes because they prey on bacterial hosts, mediate horizontal gene transfer, alter host metabolism and redistribute bacterially derived compounds via host cell lysis 1 . (nature.com)
Satellite viruses replicating in plants have small icosahedral virions and encapsidate positive-sense RNA genomes typically carrying a single gene for the capsid protein. (hal.science)
Despite a disparity in gene content, all mtDNAs encode at least two components of the mitochondrial electron transport chain, including cytochrome c oxidase I (Cox1). (biomedcentral.com)

Another viral sequence encoded a protein with 70% amino acid homology to the predicted RdRp. (virology.ws)
In an early, RNA-protein world, there would not be enzymes to degrade DNA, so a virus encoded by DNA would have a big survival advantage. (3quarksdaily.com)
The symbiosis of virus plus RNA/protein cell eventually resulted in the modern arrangement of DNA, RNA and protein. (3quarksdaily.com)
Soil Virus Offers Insight into Maintaining Microorganisms Through a collaborative effort, researchers have identified a protein in soil viruses that may promote soil health. (doe.gov)

We discuss the recent advances towards understanding the function and structure of the proteins encoded by the rudivirus genomes, their role in the virus life cycle, and outline the directions for further research on this model system. (pasteur.fr)

Dr Simona Pilotto , the lead author of the second study elaborates on her work: The inhibition of RNAP and the resulting attenuation of the transcriptome plays a crucial role in the interaction between viruses and their hosts during infection. (lon.ac.uk)

Identification of archaeal RNA viruses is important because their study could provide information about the ancestors of RNA viruses that infect eukaryotes. (virology.ws)
What is needed to resolve this question is old-fashioned virology: isolating RNA virus particles that can infect an archaeal host and produce new infectious viruses. (virology.ws)

Analysis of the RNA viral sequences revealed coding regions for a predicted RNA dependent RNA polymerase (RdRp), a hallmark of RNA viruses. (virology.ws)
It encodes an extremely large virion-associated RNA polymerase unique for bacterial viruses that became characteristic for this group. (mdpi.com)

Future studies on archaeal viruses, combined with the knowledge on viruses of bacteria and eukaryotes, should lead to a better global understanding of the diversity and evolution of virus-host interactions in the viral world. (pasteur.fr)

Characterization of promoters in archaeal genomes based on DNA structural parameters. (openwetware.org)

Latency in bacteriophage is maintained by the expression of virally encoded repressors. (lookformedical.com)

Halorubrum pleomorphic virus 1 (HRPV-1) is a single stranded DNA virus that infects the species of the archaeal genus Halorubrum. (wikipedia.org)
Most of these viruses have not yet been discovered: just over 2,000 viral species are recognized . (virology.ws)
Proteins found in any species of virus. (lookformedical.com)
The type species of ORTHOPOXVIRUS, related to COWPOX VIRUS , but whose true origin is unknown. (lookformedical.com)
Virulence Virulence The degree of pathogenicity within a group or species of microorganisms or viruses as indicated by case fatality rates and/or the ability of the organism to invade the tissues of the host. (lecturio.com)
This system is present in most archaeal species and approxi-mately half of all bacterial species. (pjmonline.org)

A Better Way to Find RNA Virus Needles in the Proverbial Database Haystacks Researchers combed through more than 5,000 data sets of RNA sequences generated from diverse environmental samples around the world, resulting in a five-fold increase of RNA virus diversity. (doe.gov)
However, the roles of viruses and the diversity of the viral community are just beginning to be understood in WWTPs. (biomedcentral.com)
This article describes the diversity and properties of these viruses. (hal.science)

Viruses, a group of non-cellular organisms, are the most abundant living entity on Earth, but depend on host cells for their own propagation [ 7 ]. (biomedcentral.com)
From such qs-c of stem-loop groups we can trace a variety of RNA secondary structures such as ribozymes, viroids, viruses, mobile genetic elements as abundant infection derived agents that provide the stem-loop societies of small and long non-coding RNAs. (philpapers.org)

However, if we could minimize this redundancy to encode additional nonstandard amino acids (NSAAs), this could permit the evolution of entirely new biological functions and possibly, new organisms. (dissertation.com)
Comparative genomics of DNA-binding transcription factors in archaeal and bacterial organisms. (openwetware.org)

Amino-acid sequence and structure comparison suggested that the enzyme belongs to a group of enzymes classified as archaeal Holliday junction-resolving enzymes, which are typically divalent metal ion-binding dimers that are able to cleave X-shaped dsDNA-Holliday junctions (Hjs). (iucr.org)

Two of these encode the structural proteins VP3 and VP4. (wikipedia.org)
Satellite viruses are a polyphyletic group of viruses encoding structural components of their virions, but incapable of completing the infection cycle without the assistance of a helper virus. (hal.science)

Instead, virus particles depend on diffusion for transportation and attachment from one host cell to another. (montana.edu)
The expelling of virus particles from the body. (lookformedical.com)

The mechanism by which latent viruses, such as genetically transmitted tumor viruses ( PROVIRUSES ) or PROPHAGES of lysogenic bacteria, are induced to replicate and then released as infectious viruses. (lookformedical.com)

RIP is encoded by the Acidianus two-tailed virus (ATV) and sterically interferes with the interaction of template DNA and transcription factors by molecular mimicry of initiation factors. (lon.ac.uk)

Genetically encoded phosphoserine incorporation programmed by the UAG codon was achieved by addition of an orthogonal translation system (OTS) consisting of an engineered elongation factor and archaeal aminoacyl-tRNA synthetase (aaRS)/tRNA pair to the normal E. coli translation machinery ( 16 ). (dissertation.com)

Open in a separate window Fig. 3 Phylogenetic tree of archaeal and Nitrosoarchaeum limnia, have one is probably not efficiently amplified by PCR due to the presence of mismatches in the primer sequences. (healthweblognews.info)

There's also some newer-fangled ways of seeing what their hosts are: do some proteomics on fairly rudely isolated host bacteria, and look for virus-specific signals, recognised from the sequence. (virology.ws)
In the Nature paper, Banfield, doctoral candidate Basem Al-Shayeb, postdoctoral fellow Marie Schoelmerich and their colleagues describe what they've learned about Borgs from sequencing Borg DNA and the DNA of their archaeal hosts. (berkeley.edu)

The isolation of a new archaeal virus, Thermoproteus Piliferous Virus 1 (TSPV1), is also presented here. (montana.edu)

Specific hypothetical schemes are developed for the functioning of the predicted prokaryotic siRNA system and for the formation of new CRISPR units with unique inserts encoding psiRNA conferring immunity to the respective newly encountered phages or plasmids. (biomedcentral.com)
The genomic component of the CRISPR-Cas system is formed by a series of variable spacers, which in some cases share sequence similarity with viruses, plasmids, or bacteria. (pjmonline.org)

DNA as a genomic storage compound originated in viruses as a way of evading the defenses of ancient cells. (3quarksdaily.com)
Genomic and morphological analyses identified vB_OliS_GJ44 as a siphovirus, however, due to the distant evolutionary relationship with any other known siphovirus, it is proposed that this virus could be classified as the type phage of a new Oceanospirivirus genus within the Siphoviridae family. (biomedcentral.com)

We identified four assembled fragments that encoded the enzymatically critical pmoC subunit of pMMOs. (nature.com)

Viral lysis of host microbes and virus-mediated HGT can regulate the biogeochemical and nutrient cycles, thus affecting the performance of AS systems. (biomedcentral.com)

To our knowledge, this is the first crystal structure of an Hj-resolving enzyme originating from a bacteriophage that can be classified as an archaeal type of Hj-resolving enzyme. (iucr.org)

Rabbitpox virus is a subspecies of VACCINIA VIRUS . (lookformedical.com)

Based on this data, a model is proposed for the maturation of the virus capsid from a noninfectious to an infectious form, by dissociation of accessory proteins. (montana.edu)
The TSPV1 virion has numerous fibrous extensions from the capsid, of varying length, that are the first observed for any virus. (montana.edu)
The capsid 2-3nm fibers likely serve to extend the effective surface area of the virus, facilitating attachment to host cells. (montana.edu)

Substances elaborated by viruses that have antigenic activity. (lookformedical.com)
Bioinformatic analysis of Chikungunya virus B-cell epitopes with high antigenic potential for vaccine development. (openwetware.org)

In another article, published in the renowned journal, Nature Communications , the researchers describe new findings that provide insights into the constant battle between microorganisms and the viruses that represent their worst enemies. (azolifesciences.com)

Direct sequencing of viral communities from the environment, known as viral metagenomics, is one approach being taken to discover archaeal viruses. (virology.ws)

By infecting and lysing host cells, viruses can affect the composition of microbial populations and facilitate the transfer of organic matter from cells to the dissolved organic matter pool via the "viral shunt" [ 9 ], and when consumed by small phagotrophs, viruses facilitate the movement of organic matter into the classical food web, which is called the "viral sweep" [ 10 ]. (biomedcentral.com)

Scanning electron micrograph of Saccharolobus islandicus cells (light blue) infected with the lemon-shaped virus STSV2 (yellow). (pasteur.fr)

15-) using a local database for identification of all viruses, bacteria and archaeal genomes extracted from the NCBI refseq database (downloaded 15/04/2017). (cdc.gov)
The resulting contigs were scanned against several BLAST ( 12 ) pre-generated databases downloaded from NCBI ( nt , tsa_nt , ref_prok_rep_genomes , ref_viruses_rep_genomes , and vector - downloaded 15/04/2017). (cdc.gov)

Sequence similarity networks of prokaryotic virus DJR MCP. (biomedcentral.com)

Every different life form on earth can probably be infected with at least one type of virus, if not many more. (virology.ws)

Activated sludge (AS) systems in wastewater treatment plants (WWTPs) harbor enormous viruses that regulate microbial metabolism and nutrient cycling, significantly influencing the stability of AS systems. (biomedcentral.com)
His particular interests include coral reef microbial ecology and viruses as both evolutionary agents and opportunistic pathogens in various environments. (academicinfluence.com)

Specific molecular components of the cell capable of recognizing and interacting with a virus, and which, after binding it, are capable of generating some signal that initiates the chain of events leading to the biological response. (lookformedical.com)
El grupo investiga las interacciones que se establecen a nivel molecular entre las plantas y algunos de sus patógenos, como los virus y los viroides. (upv.es)
El grupo contribuye al avance del conocimiento de la biología molecular de las plantas y de sus patógenos, así como al desarrollo de herramientas biotecnológicas para la protección, mejora e innovación en los cultivos. (upv.es)
J.A. Darós es Licenciado en Ciencias Biológicas, especialidad Bioquímica y Biología Molecular (1985-1990). (upv.es)
A continuación realizó una estancia postdoctoral en los EE UU durante tres años y medio (Enero 1995-Junio 1998) en el grupo del Prof. James C. Carrington en la Texas A&M University (College Station, Texas) y la Washington State University (Pullman, Washington), donde estudió distintos aspectos de la biología molecular de los potyvirus. (upv.es)
En Agosto 1998 se reincorporó como investigador postdoctoral al grupo del Prof. Ricardo Flores en el IBMCP donde investigó la biología molecular de los viroides, primero con un contrato de reincorporación del Ministerio y, posteriormente (Noviembre 2001-Junio 2004), mediante un contrato del Programa Ramón y Cajal . (upv.es)
Además ha actuado como revisor en multitud de revistas del ámbito de la biología molecular, virología, fitopatología y biología de plantas. (upv.es)

Infection appears to be productive without lysis of the host like may of the archaeal viruses. (wikipedia.org)
The ability of a pathogenic virus to lie dormant within a cell (latent infection). (lookformedical.com)

In the present review, we summarize the current knowledge on one of the emerging model systems for studies on crenarchaeal viruses, the Rudiviridae. (pasteur.fr)
The research presented here provides a substantial advancement in our knowledge of the attachment process for archaeal viruses. (montana.edu)
Despite the ecological importance of this bacteria lineage, our knowledge about the viruses infecting Oceanospirillaceae is quite few. (biomedcentral.com)

Deoxyribonucleic acid that makes up the genetic material of viruses. (lookformedical.com)
Viruses whose genetic material is RNA. (lookformedical.com)
However, the conservation of the genetic code also allows viruses to hijack host translation machinery ( 15 ) and compromise cell viability. (dissertation.com)

Furthermore, combining the previously determined atomic model for the virus, with cryo-electron tomography, a pseudo-atomic model of the interaction between the host pilus and virus was determined. (montana.edu)
Attachment to host pili is now emerging as a common theme for archaeal viruses. (montana.edu)
According to this view, ancient viruses, as with the ones today, could only make copies of themselves by succesfully infecting a host. (3quarksdaily.com)

However, owing to recent substantial research efforts by several groups, archaeal viruses are starting to gradually reveal their secrets. (pasteur.fr)

Anatomy2

Organisms18

Diseases1

Chemicals and Drugs5

Analytical, Diagnostic and Therapeutic Techniques and Equipment1

Phenomena and Processes10

Information Science2

Genes18

Genome11

Phage-encoded3

Archaea9

Eukaryotic2

Sulfolobus5

Genomes encode1

Bacterial genomes1

Gene8

Protein4

Proteins encoded1

Inhibition1

Infect2

Polymerase2

Bacteria and eukaryotes1

Characterization1

Repressors1

Species6

Diversity3

Abundant2

Organisms2

Enzymes1

Structural2

Particles2

Infectious viruses1

Transcription1

Elongation1

Sequences1

Hosts2

Isolation1

Plasmids2

Genomic2

Subunit1

Microbes1

Bacteriophage1

VACCINIA VIRUS1

Capsid3

Antigenic2

Researchers1

Metagenomics1

Viral shunt1

Islandicus1

NCBI2

Prokaryotic1

Type1

Microbial2

Molecular7

Infection2

Knowledge3

Genetic3

Host3

Reveal1