• Kitaviridae is a family of plant-infecting viruses that have multiple positive-sense, single-stranded RNA genomic segments. (bvsalud.org)
  • Hepatitis C virus (HCV), a member of the Flaviviridae family, is a single-stranded enveloped RNA virus that infects approximately 170 million people worldwide. (xiahepublishing.com)
  • The HCV genome consists of a 9.6 kb uncapped linear single-stranded RNA with positive polarity. (xiahepublishing.com)
  • SARS-CoV-2 is a spherical, enveloped, single-stranded positive RNA virus with a diameter of 80 nm-160 nm and a genome size of 29.9 kb [ 8 ]. (newvita.com)
  • (i) non-enzymatic RNA replication of a hemi-protonated cytosine-rich oligonucleotide, and (ii) specific aminoacylation of tRNA/hairpins through triple helix interactions between the helical aminoacyl stem and a single-stranded aminoacylating ribozyme. (biomedcentral.com)
  • The PepMV genome is a single-stranded RNA molecule approximately 6.4 kb in length, comprising five open reading frames (ORFs) flanked by 5' and 3' untranslated regions (UTRs) with a 5'-cap and a 3' poly-A tail. (biomedcentral.com)
  • PRRSV, a positive sense and single-stranded RNA virus, is a member of family Arteriviridae [ 1 ]. (biomedcentral.com)
  • RNA is very similar to DNA, but differs in a few important structural details: RNA is usually single stranded, while DNA is usually double stranded. (wikidoc.org)
  • First, unlike DNA which is double-stranded, RNA is a single-stranded molecule in most of its biological roles and has a much shorter chain of nucleotides. (wikidoc.org)
  • Chemical shift changes upon the addition of single-stranded RNAs (ssRNAs) identified a group of residues that form a positively charged patch on the protein surface as the binding site responsible for the previously reported affinity for nucleic acids. (pdfroom.com)
  • SARS-CoV-2 as a positive-sense single-stranded RNA coronavirus caused the global outbreak of COVID-19. (bvsalud.org)
  • The single-stranded (+)-RNA viruses comprise the largest group of viruses, which includes pathogens such as Dengue virus, Corona virus and West Nile virus. (fortunejournals.com)
  • Studies of the mechanism of Qβ infection can increase our general understanding of the single-stranded (+)-RNA viruses, which can be exploited in the pursuit to treat and prevent diseases caused by pathogenic (+)-RNA viruses. (fortunejournals.com)
  • The largest group is the single-stranded, positive sense (+)-RNA viruses, which comprises more than a third of all viruses. (fortunejournals.com)
  • Researchers found that the RNA sequences they analyzed contained a signature gene called RdRp that codes for RNA-dependent RNA polymerase-a complex enzyme designed to catalyze replication. (icr.org)
  • Kitavirus genomes encode numerous orphan open reading frames but RNA-dependent RNA polymerase and the transmembrane helix-containing protein, generically called SP24, typify a close phylogenetic link with arthropod viruses. (bvsalud.org)
  • What differentiates the replicases in the A, B and C families from repair polymerases in the X- and Y-family is the proofreading mechanism and the structure and formation of the polymerase active site. (cathdb.info)
  • The catalytic core of DNA polymerase is formed from the thumb, palm and finger domains. (cathdb.info)
  • It has a typical right-hand DNA polymerase fold, with an active site formed by a palm holding the catalytic residues, a thumb that binds the primer:template DNA and fingers interacting with incoming nucleotide, and the N and Exo domains extend from the finger toward the thumb. (cathdb.info)
  • We report RNA-catalysed RNA synthesis on structured templates when using trinucleotide triphosphates (triplets) as substrates, catalysed by a general and accurate triplet polymerase ribozyme that emerged from in vitro evolution as a mutualistic RNA heterodimer. (elifesciences.org)
  • 6 , 7 Replication of the virus is performed by an HCV-encoded RNA-dependent polymerase, which lacks proofreading capability. (xiahepublishing.com)
  • Synthesis of RNA is usually catalyzed by an enzyme - RNA polymerase , using DNA as a template. (wikidoc.org)
  • The RNA genome of SARS-CoV-2 is one of the largest RNA genomes among RNA viruses [1], comprised of a replicase gene which encodes non-structural proteins (nsps), structural proteins, and accessory proteins. (insidecorona.net)
  • Once translated, these polyproteins are cleaved by one of the two encoded proteases (3C-like protease (nsp5) or papain-like-protease (nsp3)) to yield between 15 and 16 non-structural proteins, which assemble into a large membrane-bound replicase complex (RTC). (insidecorona.net)
  • One of these non-structural proteins is nsp15, a 346 amino acid nidoviral RNA uridylate‐specific and Mn 2+ -dependent [3] endoribonuclease (NendoU). (insidecorona.net)
  • However, some scientists think that before life adopted DNA and proteins, it relied primarily on RNA. (elifesciences.org)
  • Yet, some RNA strands can also fold to form ribozymes, 3D structures that could have guided life's chemical processes the way proteins do now. (elifesciences.org)
  • All life on Earth today uses a triplet RNA code to make proteins from DNA, and these experiments showed how RNA triplets might have helped RNA sustain early life forms. (elifesciences.org)
  • RNA genome can be translated to an individual polyprotein precursor which can be processed to create 10 adult proteins by co- and post-translational digesting (Rice and Lindenbach, 2003). (findadig.com)
  • Our goal is to recapitulate RNA replication in vitro using biological relevant substrates and proteins and a biologically relevant sub-genomic replicon of HCV. (uams.edu)
  • Enzymes are usually proteins, however CATALYTIC RNA and CATALYTIC DNA molecules have also been identified. (lookformedical.com)
  • This study is to explore the biogenesis mechanism of a secondary hepatocellular carcinoma (HCC) based on the function of RNA binding proteins (RBPs)-encoding genes in the physiological microenvironment (PM). (peerj.com)
  • RNA plays several important roles in the processes of translating genetic information from deoxyribonucleic acid ( DNA ) into proteins . (wikidoc.org)
  • The coronavirus replication cycle begins with the translation of the 29-kb positive-strand genomic RNA to produce two large polyprotein species (pp1a and pp1ab), which are subse- quently cleaved to produce 15 or possibly 16 nonstructural proteins (nsp's) (11). (pdfroom.com)
  • An extensive bioinformatics analysis of the coronavirus replicase proteins by Snijder et al. (pdfroom.com)
  • We studied the course of infection by analysing the production of viral RNA, proteins and phage particles produced in the cell-free reactions. (fortunejournals.com)
  • The replication of the viral RNA was determined by RT-PCR, while the translation of the viral proteins was examined by radiolabelling, and the production of infectious phage particles was evaluated by double-layered plaque assays. (fortunejournals.com)
  • Specifically, the viral RNA was replicated, the viral proteins were translated, and infectious phage particles were produced in the cell-free infection systems. (fortunejournals.com)
  • Figure 4: Evolution of genome organization in RNA viruses. (nature.com)
  • A tick-borne segmented RNA virus contains genome segments derived from unsegmented viral ancestors. (nature.com)
  • 2022. Ribonucleotide incorporation by eukaryotic B-family replicases and its implications for genome stability. (nih.gov)
  • The viral genome (total genetic information) can be RNA or DNA. (icr.org)
  • The subsequent transition to a DNA genome could have been partly driven by the gradual rise in ocean pH, since DNA has greater stability than RNA at alkaline pH, but not at acidic pH. (biomedcentral.com)
  • The Streptococcus pyogenes Cas9 (SpCas9) nuclease can be efficiently targeted to genomic loci by means of singleguide RNAs (sgRNAs) to enable genome editing 1 - 10 . (cdc.gov)
  • The genome consists of either RNA or DNA and can be single- or double-stranded, linear or circular. (fortunejournals.com)
  • Unprecedented genomic diversity of RNA viruses in arthropods reveals the ancestry of negative-sense RNA viruses. (nature.com)
  • This study reveals the molecular variability of the virus by analyzing four genomic regions (p29, p15, MP and RNA2-intergenic region) distributed over its two RNAs. (bvsalud.org)
  • The negative-sense RNA then acts as a template to produce new positive-sense genomic RNA and subgenomic RNA. (insidecorona.net)
  • 2 Viruses enter into a host cell for replication (the process of producing two identical replicas of RNA, ribonucleic acid or DNA, deoxyribonucleic acid) and take over the cell's biological machinery. (icr.org)
  • The SARS-CoV-2's endoribonuclease (NendoU) nsp15, is an Mn 2+ dependent endoribonuclease specific to uridylate that SARS-CoV-2 uses to avoid the innate immune response by managing the stray RNA generated during replication. (insidecorona.net)
  • As a result, the loss of RNA synthesis is thought to be a knock-on effect on neighbouring polyprotein components that are critical for replication, as opposed to a genuine effect on viral replication through lack of nsp15 [6]. (insidecorona.net)
  • During viral replication, positive-sense RNA is translated to produce the viral replication complex, which replicates the positive-sense RNA to produce negative-sense RNA. (insidecorona.net)
  • RNA-catalyzed RNA replication is widely believed to have supported a primordial biology. (elifesciences.org)
  • However, RNA catalysis is dependent upon RNA folding, and this yields structures that can block replication of such RNAs. (elifesciences.org)
  • To address this apparent paradox, we have re-examined the building blocks used for RNA replication. (elifesciences.org)
  • The triplets cooperatively invaded and unraveled even highly stable RNA secondary structures, and support non-canonical primer-free and bidirectional modes of RNA synthesis and replication. (elifesciences.org)
  • Triplet substrates thus resolve a central incongruity of RNA replication, and here allow the ribozyme to synthesise its own catalytic subunit '+' and '-' strands in segments and assemble them into a new active ribozyme. (elifesciences.org)
  • For early life to be built on RNA, though, this molecule must have had the ability to make copies of itself. (elifesciences.org)
  • A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts. (lookformedical.com)
  • The phosphate groups have a negative charge each at physiological pH, making RNA a charged molecule. (wikidoc.org)
  • A second consequence of the presence of the 2'-hydroxyl group is that in conformationally flexible regions of an RNA molecule (that is, not involved in formation of a double helix), it can chemically attack the adjacent phosphodiester bond to cleave the backbone. (wikidoc.org)
  • Figure 1: RNA Cleavage as performed by nsp15 to give a 2′‐3′ cyclic phosphodiester and 5′‐hydroxyl terminus from an RNA nucleotide phosphodiester from PDB entry 1RNA. (insidecorona.net)
  • RNA nucleotides contain ribose while DNA contains deoxyribose (a type of ribose that lacks one oxygen atom), and RNA uses the nucleotide uracil in its composition, instead of thymine which is present in DNA. (wikidoc.org)
  • Koonin, E. V. The phylogeny of RNA-dependent RNA polymerases of positive-strand RNA viruses. (nature.com)
  • 2003. Evolutionary connection between the catalytic subunits of DNA-dependent RNA polmerases and eukaryotic RNA-dependent RNA polymerases. (icr.org)
  • RNA is transcribed from DNA by enzymes called RNA polymerases and is generally further processed by other enzymes, some of them guided by non-coding RNAs . (wikidoc.org)
  • Previous studies have shown that the nsp11 of equine arteritis virus(EAV), which is another member of family Arteriviridae, may play a key role in viral RNA synthesis and additional functions in the viral life cycle [ 8 ]. (biomedcentral.com)
  • One type of RNA acts as a messenger between DNA and the protein synthesis complexes known as ribosomes , others form vital portions of the structure of ribosomes, act as essential carrier molecules for amino acids to be used in protein synthesis, or change which genes are active. (wikidoc.org)
  • Here we profile the transcriptomes of over 220 invertebrate species sampled across nine animal phyla and report the discovery of 1,445 RNA viruses, including some that are sufficiently divergent to comprise new families. (nature.com)
  • The identified viruses fill major gaps in the RNA virus phylogeny and reveal an evolutionary history that is characterized by both host switching and co-divergence. (nature.com)
  • Figure 2: Phylogenetic diversity of RNA viruses. (nature.com)
  • RNA viruses are clearly important in our world, but we usually only study a tiny slice of them- the few hundred that harm humans, plants and animals. (icr.org)
  • state a new phylum called Taraviricota is supposedly a missing link in early RNA virus evolution, 4 but Taraviricota is still composed of 100% viruses, and their RNA has always been RNA. (icr.org)
  • 2022. Cryptic and abundant marine viruses at the evolutionary origins of Earth's RNA virome. (icr.org)
  • The group of (+)-RNA viruses includes a number of pathogenic viruses such as Polio virus, Hepatitis A and C, Dengue virus and Severe Acute Respiratory Syndrome coronavirus [3]. (fortunejournals.com)
  • The (+)-RNA viruses have been used in the development of vaccines, as imaging tools and in virus inactivation studies [4, 5]. (fortunejournals.com)
  • A standard curve of the 73 nt amplicon MP gene was developed using known 10(10)-10(1) copies of in vitro synthesized RNA transcript to estimate the copy number of RNA transcript in the citrus leprosis samples. (bvsalud.org)
  • To evaluate the quality of the total RNA extracts, NADH dehydrogenase gene specific primers (nad5) and probe were included in reactions as an internal control. (bvsalud.org)
  • This process produces short and long double-stranded RNA intermediates with polyuridine tracts at the 5′ end which can be recognized by pattern recognition receptors in the host cell such as RIG-I-like receptors (RLRs), protein kinase R (PKR), oligoadenylate synthases (OASes), and melanoma differentiation-associated gene 5 (MDA5). (insidecorona.net)
  • The concept of an RNA world - an early stage of evolution where RNA functioned as both gene and catalyst - has wide, though certainly not unanimous, support among those who study the origin of life. (biomedcentral.com)
  • Two sequence motifs, residues 1074-1077 in the long segment of the L-shaped thumb, and residues 1130-1150 in the tip of the thumb, form a continuous protein interface that tracks the position of the phosphodiester backbone of the RNA primer. (cathdb.info)
  • This is supported by the enhanced stability at acidic pH of not only the RNA phosphodiester bond but also of the aminoacyl-(t)RNA and peptide bonds. (biomedcentral.com)
  • However, one difficulty with this attractive scenario is the instability of the phosphodiester bond of RNA at alkaline pH [ 10 ] (Figure 1 ), suggesting that RNA is more likely to have evolved in an environment of lower pH. (biomedcentral.com)
  • The RNA phosphodiester bond is most stable at pH 4-5 at 90°C . Hydrolysis of the dinucleoside 3',5'-UpU at 90°C as a function of pH. (biomedcentral.com)
  • Helicases are enzymes that manipulate DNA and RNA in all aspects of nucleic acid metabolism. (uams.edu)
  • Energy Producing Catalytic molecules are Enzymes. (answers.com)
  • Enzymes which are immobilized on or in a variety of water-soluble or water-insoluble matrices with little or no loss of their catalytic activity. (lookformedical.com)
  • Corresponding DLBCL formalin fixed, paraffin embedded tissues have been collected for IHC detection of PI3K catalytic subunits. (mirnaarray.com)
  • Subgenomic RNA consists of smaller transcribed sections of RNA produced by initiating transcription in the middle of the template strand (internal initiation), falling off the template strand before reaching the 5' stop codon (premature termination), or by jumping off the template strand and reinitiating transcription further down the template (discontinuous transcription). (insidecorona.net)
  • We explored several strategies for vector development including coat protein (CP) replacement, duplication of the CP subgenomic promoter (SGP) and the creation of a fusion protein using the foot-and-mouth disease virus (FMDV) 2A catalytic peptide. (biomedcentral.com)
  • Ribonucleic acid or RNA is a nucleic acid , consisting of many nucleotides that form a polymer . (wikidoc.org)
  • Nsp15 is conserved across coronavirus family members [6], to the point where it has been proposed as a universal genetic marker to distinguish nidoviruses [7] from all other RNA virus families. (insidecorona.net)
  • Like DNA, strands of RNA contain genetic data. (elifesciences.org)
  • Since it is "generally" agreed that there was a living organism with a genetic system based entirely on RNA [4,5] in the "shape" of a LUCA, our network's aim is to "peel" back the "metaphoric onion of LUCA" from the first emergence of life to the point of preRNA chemistry [6]. (norcel.net)
  • 2022. Ribonucleotide incorporation by eukaryotic B-family DNA replicases and its consequences. (nih.gov)
  • Partial Order Optimum Likelihood (POOL), a machine learning method that uses input features from Theoretical Microscopic Titration Curve Shapes (THEMATICS), was used to identify amino acid residues most likely involved in catalytic activity. (bvsalud.org)
  • For instance, determination of the structure of the ribosome - an enzyme that catalyzes peptide bond formation - revealed that its active site is composed entirely of RNA. (wikidoc.org)
  • DENV encodes a positive-strand RNA around 11 kb long with a sort 1 cover, m7GpppA(2-Om) in the 5-end but missing a poly(A) tail in the 3end. (findadig.com)
  • High-throughput RNA sequencing (RNA-seq) and bioinformatics were used to identify the potential microorganisms. (asm.org)
  • The samples were analyzed using the technology of RNA-seq and bioinformatics. (peerj.com)
  • The interactions between the thumb domain and the RNA primer are concentrated in a contiguous region of five nucleotides, from position two to six of the RNA primer and involve solely the ribose and phosphate moieties of the RNA backbone. (cathdb.info)
  • Pol alpha exploits the wide, shallow nature of the minor groove of the RNA/DNA helix with a series of hydrophobic contacts involving the side chains of Met1131, Leu1133, Tyr1140, Pro1141, Met1146, which recognise the C3'-endo conformation of the ribose moieties of RNA nucleotides in position four to six. (cathdb.info)
  • The most important structural feature of RNA, that distinguishes it from DNA is the presence of a hydroxyl group at the 2'-position of the ribose sugar. (wikidoc.org)
  • Secondly, while DNA contains deoxyribose , RNA contains ribose , (there is no hydroxyl group attached to the pentose ring in the 2' position in DNA, whereas RNA has two hydroxyl groups). (wikidoc.org)
  • this has led scientists to try to artificially create RNA replicase ribozymes that could copy themselves. (elifesciences.org)
  • Yet, although ribozymes can be made to copy straight RNA templates this way, folded RNA templates - including the replicase ribozyme itself - impede copying. (elifesciences.org)
  • The fusion protein incorporating the FMDV 2A catalytic peptide gave by far the best results, maintaining stability through serial passages and allowing the accumulation of GFP to 0.2-0.4 g per kg of leaf tissue. (biomedcentral.com)
  • A stable PepMV vector was generated by expressing the transgene as a CP fusion using the sequence encoding the foot-and-mouth disease virus (FMDV) 2A catalytic peptide to separate them. (biomedcentral.com)
  • We performed northern blot analyses for the guide RNA truncations and found increased levels of expression for the longer tracrRNA sequences, suggesting that improved target cleavage was at least partially due to higher sgRNA expression or stability ( Fig. 1c ). (cdc.gov)
  • However, RNA is most stable at pH 4-5 and is unstable at alkaline pH, raising the possibility that RNA may have first arisen in the acidic ocean itself (possibly near an acidic hydrothermal vent), acidic volcanic lake or comet pond. (biomedcentral.com)
  • These hydroxyl groups make RNA less stable than DNA because it is more prone to hydrolysis . (wikidoc.org)
  • The RNAs play important roles in the pathological and physiological tissues including cancer. (peerj.com)
  • The 2014 NoR HGT & LUCA meeting was entitled: "the routes of emergence of life from LUCA during the RNA and viral world" and was held at the University of Leeds, UK, October 2014. (norcel.net)
  • Current knowledge of RNA virus biodiversity is both biased and fragmentary, reflecting a focus on culturable or disease-causing agents. (nature.com)
  • Together, these data present a view of the RNA virosphere that is more phylogenetically and genomically diverse than that depicted in current classification schemes and provide a more solid foundation for studies in virus ecology and evolution. (nature.com)
  • The research is part of the Tara Oceans Consortium and has identified 5,500 new RNA virus species that represent all five known RNA virus phyla (a taxonomic category). (icr.org)
  • Ocean water samples yield treasure trove of RNA virus data. (icr.org)
  • Figure 1: The frequency and diversity of viral RNA transcripts in invertebrate transcriptomes. (nature.com)
  • These structures show that a nsp15 monomer consist of three conserved domains, the N-terminal oligomerization domain, the middle domain, and the catalytic NendoU domain. (insidecorona.net)
  • For example, these triplets work together to bind tightly to RNA strands and unravel structures that block RNA copying. (elifesciences.org)
  • Using three-letter 'triplet' building blocks, this new ribozyme can copy various folded RNA strands, including the active part of its own sequence. (elifesciences.org)
  • We find that SpCas9 tolerates mismatches between guide RNA and target DNA at different positions in a sequence-dependent manner, sensitive to the number, position and distribution of mismatches. (cdc.gov)
  • Like DNA, most biologically active RNAs including tRNA, rRNA, snRNAs and other non-coding RNAs are extensively base paired to form double stranded helices. (wikidoc.org)
  • Here, we firstly explored the effect of over-expression of nsp11 on PRRSV infection and found that over-expression of nsp11 enhanced the PRRSV titers while the small interfering RNA (siRNAs) specifically targeting nsp11 could reduce the PRRSV titers in MARC-145 cells. (biomedcentral.com)
  • Notably, no viral RNA was detected in various organs of the Group 2 pigs 16 days post-infection with HP-PRRSV, except in one pig. (biomedcentral.com)
  • Biochemical techniques were used to engineer a ribozyme that copies RNA strands by adding letters not one-by-one, but three-by-three. (elifesciences.org)