• During transcription, a DNA sequence is read by an RNA polymerase, which produces a complementary, antiparallel RNA strand called a primary transcript. (wikipedia.org)
  • Transcription proceeds in the following general steps: RNA polymerase, together with one or more general transcription factors, binds to promoter DNA. (wikipedia.org)
  • RNA polymerase generates a transcription bubble, which separates the two strands of the DNA helix. (wikipedia.org)
  • RNA polymerase adds RNA nucleotides (which are complementary to the nucleotides of one DNA strand). (wikipedia.org)
  • RNA sugar-phosphate backbone forms with assistance from RNA polymerase to form an RNA strand. (wikipedia.org)
  • This directionality is because RNA polymerase can only add nucleotides to the 3' end of the growing mRNA chain. (wikipedia.org)
  • In this study we expressed plant DCL4 in Saccharomyces cerevisiae , an RNAi-depleted organism, in which we could highlight the role of dicing as neither Argonautes nor RNA-dependent RNA polymerase is present. (biomedcentral.com)
  • The viral RNA dependent RNA polymerase (L) binds to a promoter on each encapsidated segment, and transcribes the mRNAs. (expasy.org)
  • 1. RNA-directed DNA polymerase, hence called RT. (biologydiscussion.com)
  • The interface of the 66 kDa and 51 kDa monomers provides a track from the polymerase active site to the RNaseH active site, and allow for the concomitant destruction of the RNA primer template strand directly after it has been copied (Fig. 13.15). (biologydiscussion.com)
  • Viral RNA polymerase, a nonstructural protein, has been termed "virus infection associated antigen" (VIAA) for diagnostic purposes but is more accurately termed "FMDV nonstructural protein 3D. (wikisource.org)
  • For instance, the genome of a negative-sense single-stranded RNA (ssRNA -) virus may be a template for a positive-sense single-stranded RNA (ssRNA +)[clarification needed]. (wikipedia.org)
  • The complete genome sequence of the new Israeli tobamovirus showed high sequence identity to the Jordanian isolate Rabbit Polyclonal to NCR3 of tomato brown rugose fruit virus. (thekingsfoundation.org)
  • are characterized by a typical rod-shaped particle morphology encapsulating a single stranded RNA (+ssRNA) sense genome of 6.2 to 6.4kb encoding four ORFs. (thekingsfoundation.org)
  • Non-enveloped, spherical, about 30 nm in diameter, pseudo T=3 icosahedral capsid surrounding the naked RNA genome. (expasy.org)
  • Monopartite, linear ssRNA(+) genome of 7.8 kb, polyadenylated, composed of a single ORF encoding a polyprotein. (expasy.org)
  • The virion RNA is infectious and serves as both the genome and viral messenger RNA. (expasy.org)
  • The dsRNA genome is transcribed/replicated thereby providing viral mRNAs/new ssRNA(+) genomes. (expasy.org)
  • 51) provided detailed annotations of the then- recently sequenced SARS-CoV genome (35, 47), including the identification of a domain unique to SARS-CoV and the pre- diction of the ADP-ribose-1�-phosphatase (ADRP) activity of the X domain (since shown to be one of the macrodomains). (pdfroom.com)
  • The genome is segmented and consists of four segments of linear negative-sense and single-stranded RNA. (expasy.org)
  • 4. The primer then 'jumps' to the 3′ end of the viral genome and the newly synthesized DNA strands hybridizes to the complementary R region on the RNA. (biologydiscussion.com)
  • The genome consists of either RNA or DNA and can be single- or double-stranded, linear or circular. (fortunejournals.com)
  • After translation of their mRNA-sense genomic RNA(s), the viral RNA and the viral replication proteins are recruited to the site of viral replication in membranous compartments. (prolekarniky.cz)
  • The single genomic RNA codes for two replication proteins, p33 and p92 pol , which are sufficient to support TBSV replicon (rep)RNA replication in yeast ( Saccharomyces cerevisiae ) model host [13] , [14] . (prolekarniky.cz)
  • Viral genomic RNA has a viral protein (VPg) at its 5' end instead of a methylated nucleotide cap structure. (expasy.org)
  • Upon endosomal acidification, the capsid releases VP4 that opens a pore in the host endosomal membrane and the viral genomic RNA penetrates into the host cell cytoplasm. (expasy.org)
  • New genomic RNA is believed to be packaged into preassembled procapsids . (expasy.org)
  • Acts by degrading the 5'-polyuridines generated during replication of the poly(A) region of viral genomic and subgenomic RNAs. (icr.ac.uk)
  • 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)
  • Replication of plus-strand RNA viruses depends on recruited host factors that aid several critical steps during replication. (prolekarniky.cz)
  • Thus, two small RNA viruses, which do not code for their own helicases, seems to recruit a host RNA helicase to aid their replication in infected cells. (prolekarniky.cz)
  • All eukaryotic plus-stranded (+)RNA viruses have similar replication cycles in infected cells. (prolekarniky.cz)
  • For efficient replication, (+)RNA viruses recruit numerous host proteins [1] - [5] . (prolekarniky.cz)
  • Infections caused by several positive-stranded RNA viruses allow the characterization of DCLs involved in the RNA-silencing-based antiviral immune responses of plants. (biomedcentral.com)
  • Class VI viruses ssRNA-RT, also called the retroviruses are RNA reverse transcribing viruses with a DNA intermediate. (biologydiscussion.com)
  • 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)
  • 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)
  • These viruses are small (22-30 nm), nonenveloped, and labile below pH 7.0, and they have single-stranded positivesense RNA with approximately 8450 nucleotides that serve as messenger RNA. (wikisource.org)
  • Its ATPase activity is strongly stimulated by poly(U), poly(dT), poly(C), poly(dA), but not by poly(G)., The exoribonuclease acts on both ssRNA and dsRNA in a 3' to 5' direction. (icr.ac.uk)
  • If not degraded, poly(U) RNA would hybridize with poly(A) RNA tails and activate host dsRNA sensors (By similarity). (icr.ac.uk)
  • The genetic material can be ssRNA (single stranded RNA), dsRNA , ssDNA , or dsDNA between 5 and 500 kilo base pairs long with either circular or linear arrangement. (wikidoc.org)
  • We have therefore tested the DCL4 functionality in processing exogenous dsRNA-like substrates, such as a replicase-assisted viral replicon defective-interfering RNA and RNA hairpin substrates, or endogenous antisense transcripts. (biomedcentral.com)
  • Plant Dicer-like proteins (DCLs) are RNase III, double-stranded RNA (dsRNA)-specific endonucleases with specialized functions in producing short (s)RNAs of 21- to 24-nucleotides (nt), including micro (mi)RNAs and short interfering (si)RNAs of endogenous or viral origin. (biomedcentral.com)
  • These led to the conclusion that DCL4 and DCL2 act redundantly and one of the two alone is sufficient to perceive dsRNA of viral origin, process it into siRNA of viral origin (vsiRNAs) and initiate the plant RNA silencing-based antiviral defense [ 14 ]. (biomedcentral.com)
  • Double-stranded RNA (dsRNA) is a potent initiator of gene silencing in a diverse group of organisms that includes plants, Caenorhabditis elegans, Drosophila and mammals. (biomedcentral.com)
  • We have previously shown and patented that mechanical inoculation of in vitro -transcribed dsRNA derived from viral sequences specifically prevents virus infection in plants. (biomedcentral.com)
  • In Drosophila melanogaster , the RNase III-like enzyme Dicer cleaves the dsRNA silencing trigger into RNA species of approximately 21 to 25 nucleotides. (biomedcentral.com)
  • Thus, the PTGS degradation machinery in plants would lead to the elimination of the viral RNA, as long as the dsRNA trigger contains sequences homologous to the invading virus. (biomedcentral.com)
  • We have previously shown that dsRNA derived from viral sequences can interfere with virus infection in a sequence-specific manner by directly delivering in vitro -transcribed dsRNA into leaf cells by mechanical inoculation [ 19 ]. (biomedcentral.com)
  • The segments of DNA transcribed into RNA molecules that can encode proteins are said to produce messenger RNA (mRNA). (wikipedia.org)
  • This is because the positive-sense strand contains the sequence information needed to translate the viral proteins needed for viral replication. (wikipedia.org)
  • Altogether, the two host factors enhance TBSV replication synergistically by interacting with the viral (−)RNA and the replication proteins. (prolekarniky.cz)
  • Among the identified host proteins are RNA-binding proteins, such as translation factors, ribosomal proteins and RNA-modifying enzymes [1] . (prolekarniky.cz)
  • The co-opted host proteins likely affect several steps in viral RNA replication, including the assembly of the replicase complex and/or viral RNA synthesis. (prolekarniky.cz)
  • ORF1 and ORF2 are separated by a leaky stop codon and encode non-structural proteins that form the replicase complex. (thekingsfoundation.org)
  • The polyprotein is initially processed by the viral protease into various precursor and mature proteins to yield the structural proteins, replicase, VPg, and a number of proteins that modify the host cell, ultimately leading to cell lysis . (expasy.org)
  • This binding site is similar to the ssRNA-binding site of the sterile alpha motif domain of the Saccharomyces cerevisiae Vts1p protein, although the two proteins do not share a common globular fold. (pdfroom.com)
  • An extensive bioinformatics analysis of the coronavirus replicase proteins by Snijder et al. (pdfroom.com)
  • In plants, RNase III Dicer-like proteins (DCLs) act as sensors of dsRNAs and process them into short 21- to 24-nucleotide (nt) (s)RNAs. (biomedcentral.com)
  • This idea was very unpopular at first as it contradicted the central dogma of molecular biology which states that DNA is transcribed into RNA which is then translated into proteins. (biologydiscussion.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)
  • In virology, the term transcription may also be used when referring to mRNA synthesis from an RNA molecule (i.e., equivalent to RNA replication). (wikipedia.org)
  • clarification needed] A DNA transcription unit encoding for a protein may contain both a coding sequence, which will be translated into the protein, and regulatory sequences, which direct and regulate the synthesis of that protein. (wikipedia.org)
  • This also removes the need for an RNA primer to initiate RNA synthesis, as is the case in DNA replication. (wikipedia.org)
  • The in vitro data show that Ded1p plays a role in enhancing plus-strand synthesis by the viral replicase. (prolekarniky.cz)
  • The data obtained with wt and ATPase deficient Ded1p mutants support the model that Ded1p unwinds local structures at the 3′-end of the TBSV (−)RNA, rendering the RNA compatible for initiation of (+)-strand synthesis. (prolekarniky.cz)
  • Plays a role in viral RNA synthesis (PubMed:32358203, PubMed:32277040, PubMed:32438371, PubMed:32526208). (icr.ac.uk)
  • 6. Once the strand is completed, second strand synthesis is initiated from the viral RNA. (biologydiscussion.com)
  • The approach required the in vitro synthesis of large amounts of RNA involving high cost and considerable labour. (biomedcentral.com)
  • VPg is removed from the viral RNA, which is then translated into a processed polyprotein. (expasy.org)
  • As opposed to DNA replication, transcription results in an RNA complement that includes the nucleotide uracil (U) in all instances where thymine (T) would have occurred in a DNA complement. (wikipedia.org)
  • In this paper, we show that an essential translation factor, Ded1p DEAD-box RNA helicase of yeast, directly affects replication of Tomato bushy stunt virus (TBSV). (prolekarniky.cz)
  • However, the functions of host factors in (+)RNA virus replication are known only for a small number of host factors [1] - [9] . (prolekarniky.cz)
  • Multifunctional protein involved in the transcription and replication of viral RNAs. (icr.ac.uk)
  • May participate in viral replication by acting as a ssRNA-binding protein (By similarity). (icr.ac.uk)
  • Conversely, DCL4 did not efficiently process a replicase-assisted viral replicon in vivo, providing evidence that viral RNAs are not accessible to DCL4 in membranes associated in active replication. (biomedcentral.com)
  • In addition, we have developed an in vitro assay for Flock house virus (FHV), a small RNA virus of insects, that also demonstrated positive effect on FHV replicase activity by the added Ded1p helicase. (prolekarniky.cz)
  • The simplest form of RNA silencing, widely known as RNA interference (RNAi), is conserved in diverse eukaryotic species, including the fungal kingdom, but has been lost in the model budding yeast, Saccharomyces cerevisiae [ 15 ]. (biomedcentral.com)
  • The replicase polyprotein of coronaviruses is a multifunctional protein: it contains the activities necessary for the transcription of negative stranded RNA, leader RNA, subgenomic mRNAs and progeny virion RNA as well as proteinases responsible for the cleavage of the polyprotein into functional products. (icr.ac.uk)
  • The papain-like proteinase 1 (PLP1) and papain-like proteinase 2 (PLP2) are responsible for the cleavages located at the N-terminus of the replicase polyprotein. (icr.ac.uk)
  • Responsible for the majority of cleavages as it cleaves the C-terminus of replicase polyprotein at 11 sites. (icr.ac.uk)
  • Responsible for the cleavages located at the N-terminus of the replicase polyprotein. (icr.ac.uk)
  • Cleaves the C-terminus of replicase polyprotein at 11 sites (PubMed:32321856). (icr.ac.uk)
  • Other stretches of DNA may be transcribed into small non-coding RNAs such as microRNA, transfer RNA (tRNA), small nucleolar RNA (snoRNA), small nuclear RNA (snRNA), or enzymatic RNA molecules called ribozymes as well as larger non-coding RNAs such as ribosomal RNA (rRNA), and long non-coding RNA (lncRNA). (wikipedia.org)
  • Ribosomal skipping is used at the junction of the 2A and downstream sequence. (expasy.org)
  • Both DNA and RNA are nucleic acids, which use base pairs of nucleotides as a complementary language. (wikipedia.org)
  • Primers for RT-LAMP or RT-RPA can be designed for specific viral RNA sequences, and the amplification methods are used before the Cas enzyme detection step, to multiply detection signals from the specific nucleic acid sequences. (nature.com)
  • Their genomes consist of two molecules of positive sense single stranded RNA with a 5′ cap and 3′ polyadenylated tail. (biologydiscussion.com)
  • We also find that Ded1p is a component of the tombusvirus replicase complex and Ded1p binds to the 3′-end of the viral minus-stranded RNA. (prolekarniky.cz)
  • 2. Complementary DNA then binds to the U5 (non-coding region) and R region (a direct repeat found at both ends of the RNA molecule) of the viral RNA. (biologydiscussion.com)
  • Viral mRNAs less susceptible to nsp1-mediated inhibition of translation, because of their 5'-end leader sequence (PubMed:32908316, PubMed:33080218). (icr.ac.uk)
  • Like other DNA and RNA polymerases, RT synthesizes polynucleotides in the 5′ to 3′ direction. (biologydiscussion.com)
  • Ribonucleic acid (RNA) has multiple roles in cellular functions, from coding genes to non-coding regulatory activities. (biomedcentral.com)
  • Reverse transcription is the process of making a double stranded DNA (deoxyribonucleic acid) molecule from a single stranded RNA (ribonucleic acid) template. (biologydiscussion.com)
  • A designed general tobamovirus primer set: F-3666(TobGen) and R-4718(TobGen), encompassing the variable nucleotide sequences was used Atrial Natriuretic Factor (1-29), chicken for species identification followed by amplicon sequencing using Sanger analysis. (thekingsfoundation.org)
  • Nsp9 is a ssRNA-binding protein. (icr.ac.uk)
  • 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)
  • Quantify DNA, RNA, and protein in seconds using only 1-2 µL of sample-no need for dilution. (thermofisher.cn)
  • The complementary RNA is created in the opposite direction, in the 5' → 3' direction, matching the sequence of the sense strand except switching uracil for thymine. (wikipedia.org)
  • After the assembly of the membrane-bound viral replicase complexes (VRC), the viral replicase uses the viral RNA as a template to produce complementary (−)RNA. (prolekarniky.cz)
  • 5. The first strand of complementary DNA (cDNA) is extended and the majority of viral RNA is degraded by RNAse H. (biologydiscussion.com)
  • Transcription is the process of copying a segment of DNA into RNA. (wikipedia.org)
  • Quantitative real-time PCR with reverse transcription (RT-qPCR), which measures the quantity of viral RNAs, remains the gold-standard technique for SARS-CoV-2 virus detection 1 . (nature.com)
  • The results all together confirm the role of sense/antisense RNA-based regulation of gene expression, expanding the sense/antisense atlas of S. cerevisiae . (biomedcentral.com)
  • A Co-Opted DEAD-Box RNA Helicase Enhances Tomb. (prolekarniky.cz)
  • The helicase which contains a zinc finger structure displays RNA and DNA duplex-unwinding activities with 5' to 3' polarity. (icr.ac.uk)
  • In turn, miRNAs and siRNAs guide the effector Argonautes (AGOs)-containing complexes to silence RNA target transcripts. (biomedcentral.com)
  • The latter function is associated with the ability of RNA to form double-stranded (ds) or ds-like secondary structures. (biomedcentral.com)
  • This was followed by evidence for double stranded RNA by Weismann and August in 1968. (biologydiscussion.com)
  • TIF) pone.0170429.s005.TIF (872K) GUID:?E856E7A8-B3BB-4D21-9310-78760577F018 S1 Table: Primer sets for next generation sequencing (NGS) validation. (thekingsfoundation.org)
  • The initial information came from study of tobacco mosaic virus (TMV) in virology that, only RNA can act as genetic material, can infect, can produce complete virus, and finally isolation of replicas. (biologydiscussion.com)
  • Posttranscriptional gene silencing (PTGS) in plants is a homology-dependent RNA degradation system designed to act as a natural defence barrier against virus infections [ 1 ]. (biomedcentral.com)
  • Next, we sequenced the full-length cDNA of I. scapularis aquaporin 1 (IsAQP1) and expressed it heterologously in Xenopus oocytes to functionally characterize its permeability to water and solutes. (bvsalud.org)
  • To learn more about isolation of viral RNA for SARS-CoV-2 research, visit the Sample Prep section on the Epidemiological Research page . (thermofisher.cn)
  • The problem is exacerbated if non-sequence-specific probes, such as pH-sensitive dyes, are used for the detection 6 . (nature.com)
  • SARS-CoV-2, the virus responsible for COVID-19, is an enveloped, non-segmented, single-stranded positive-sense RNA (+ssRNA) virus and a newly identified β-coronavirus. (thermofisher.cn)
  • a SS RNA = single-stranded RNA. (wikisource.org)
  • 3. A domain on the reverse transcriptase enzyme called RNAse H degrades the 5′ end of the RNA which removes the U5 and R region. (biologydiscussion.com)
  • The enzyme is a heterodimer consisting of 66kDa and 51kDa subunits.The two polypeptides have identical N-terminal sequences, indicating that the 51 kDa unit is cleaved from 66 kDa unit. (biologydiscussion.com)
  • Hydrogen bonds of the RNA-DNA helix break, freeing the newly synthesized RNA strand. (wikipedia.org)
  • The non-template (sense) strand of DNA is called the coding strand, because its sequence is the same as the newly created RNA transcript (except for the substitution of uracil for thymine). (wikipedia.org)
  • The RNA may remain in the nucleus or exit the cytoplasm through the nuclear pore complex. (wikipedia.org)
  • RT-RPA and RT-LAMP are highly sensitive methods, but can suffer from nonspecific amplification under isothermal conditions, leading to false-positive results when used for viral RNA detections. (nature.com)
  • Within a detection limit of 42 RNA copies per reaction, SHERLOCK was 100% specific and 100% sensitive with a fluorescence readout, and 100% specific and 97% sensitive with a lateral-flow readout. (nature.com)
  • The Invitrogen Qubit Fluorometer is designed to quickly and specifically quantify DNA or RNA. (thermofisher.cn)
  • the sequence after ("downstream" from) the coding sequence is called the three prime untranslated regions (3'UTR). (wikipedia.org)
  • In addition, next generation sequencing of total small RNA was performed on two cultivars grown in two different locations. (thekingsfoundation.org)
  • Other segments of DNA are copied into RNA molecules called non-coding RNAs (ncRNAs). (wikipedia.org)
  • Furthermore, wheat germ extracts have recently been shown to recapitulate in vitro many aspects of RNA silencing in animals [ 18 ]. (biomedcentral.com)