RNA-dependent RNA polymerase

RNA依存性RNA・リメラーゼ

関

RNA replicase

WordNet

1. relying on or requiring a person or thing for support, supply, or what is needed; "dependent children"; "dependent on moisture"
2. addicted to a drug (同)dependant, drug-addicted, hooked, strung-out
3. contingent on something else (同)dependant, qualified
4. (of a clause) unable to stand alone syntactically as a complete sentence; "a subordinate (or dependent) clause functions as a noun or adjective or adverb within a sentence" (同)subordinate
5. the 18th letter of the Roman alphabet (同)r
6. an enzyme that catalyzes the formation of new DNA and RNA from an existing strand of DNA or RNA

PrepTutorEJDIC

1. 『頼っている』,依存している,従属している / 扶養される人(家族)
2. resistance / 17歳以下父兄同伴映画の表示 / rook
3. ribonucleic acid・リボ核酸

Wikipedia preview

出典(authority):フリー百科事典『ウィキペディア（Wikipedia）』「2014/09/26 03:56:46」(JST)

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RNA-directed RNA polymerase
RNA Replicase structure PDB 3PHU.
Identifiers
EC number	2.7.7.48
CAS number	9026-28-2
Databases
IntEnz	IntEnz view
BRENDA	BRENDA entry
ExPASy	NiceZyme view
KEGG	KEGG entry
MetaCyc	metabolic pathway
PRIAM	profile
PDB structures	RCSB PDB PDBe PDBsum
Gene Ontology	AmiGO / EGO
Search PMC articles PubMed articles NCBI proteins

RNA-directed RNA polymerase, flaviviral
Identifiers
Symbol	RNA_pol_flaviviral
Pfam	PF00972
InterPro	IPR000208
Available protein structures: Pfam structures PDB RCSB PDB; PDBe; PDBj PDBsum structure summary

RNA-dependent RNA polymerase (RdRp), (RDR), or RNA replicase, is an enzyme that catalyzes the replication of RNA from an RNA template. This is in contrast to a typical DNA-dependent RNA polymerase, which catalyzes the transcription of RNA from a DNA template.

RNA-dependent RNA polymerase (RdRp) is an essential protein encoded in the genomes of all RNA-containing viruses with no DNA stage that have sense negative RNA. It catalyses synthesis of the RNA strand complementary to a given RNA template. The RNA replication process is a two-step mechanism. First, the initiation step of RNA synthesis begins at or near the 3' end of the RNA template by means of a primer-independent (de novo), or a primer-dependent mechanism that utilizes a viral protein genome-linked (VPg) primer. The de novo initiation consists in the addition of a nucleotide tri-phosphate (NTP) to the 3'-OH of the first initiating NTP. During the following so-called elongation phase, this nucleotidyl transfer reaction is repeated with subsequent NTPs to generate the complementary RNA product.

History

Viral RdRPs were discovered in the early 1960s from studies on mengovirus and polio virus when it was observed that these viruses were not sensitive to actinomycin D, a drug that inhibits cellular DNA-directed RNA synthesis. This lack of sensitivity suggested that there is a virus-specific enzyme that could copy RNA from an RNA template and not from a DNA template.

The most famous example of RdRP is that of the polio virus. The viral genome is composed of RNA, which enters the cell through receptor-mediated endocytosis. From there, the RNA is able to act as a template for complementary RNA synthesis, immediately. The complementary strand is then, itself, able to act as a template for the production of new viral genomes that are further packaged and released from the cell ready to infect more host cells. The advantage of this method of replication is that there is no DNA stage; replication is quick and easy. The disadvantage is that there is no 'back-up' DNA copy.

Many RdRPs are associated tightly with membranes and are, therefore, difficult to study. The best-known RdRPs are polioviral 3Dpol, vesicular stomatitis virus L, and hepatitis C virus NS5B protein.

Many eukaryotes also have RdRPs involved in an amplification of RNA interference. In them RdRP transcribes secondary- siRNAs, which in turn are bound by class 3 Argonauts (SAGO) to repress target RNA. In fact these same RdRPs that are used in the defense mechanisms can be usurped by RNA viruses for their benefit.

RdRps are highly conserved throughout viruses and is even related to telomerase, though the reason for such high conservation in such diverse organisms is an ongoing question as of 2009. The similarity has led to speculation that viral RdRps are ancestral to human telomerase.

Structure

All the RNA-directed RNA polymerases, and many DNA-directed polymerases, employ a fold whose organization has been likened to the shape of a right hand with three subdomains termed fingers, palm, and thumb. Only the palm subdomain, composed of a four-stranded antiparallel beta-sheet with two alpha-helices, is well conserved among all of these enzymes. In RdRp, the palm subdomain comprises three well-conserved motifs (A, B, and C). Motif A (D-x(4,5)-D) and motif C (GDD) are spatially juxtaposed; the Asp residues of these motifs are implied in the binding of Mg2+ and/or Mn2+. The Asn residue of motif B is involved in selection of ribonucleoside triphosphates over dNTPs and, thus, determines whether RNA rather than DNA is synthesized. The domain organization and the 3D structure of the catalytic centre of a wide range of RdPps, even those with a low overall sequence homology, are conserved. The catalytic centre is formed by several motifs containing a number of conserved amino acid residues.

Classification

There are 4 superfamilies of viruses that cover all RNA-containing viruses with no DNA stage:

• Viruses containing positive-strand RNA or double-strand RNA, except retroviruses and Birnaviridae: viral RNA-directed RNA polymerases including all positive-strand RNA viruses with no DNA stage, double-strand RNA viruses, and the Cystoviridae, Reoviridae, Hypoviridae, Partitiviridae, Totiviridae families
• Mononegavirales (negative-strand RNA viruses with non-segmented genomes)
• Negative-strand RNA viruses with segmented genomes, i.e., Orthomyxoviruses (including influenza A, B, and C viruses, Thogotoviruses, and the infectious salmon anemia virus), Arenaviruses, Bunyaviruses, Hantaviruses, Nairoviruses, Phleboviruses, Tenuiviruses and Tospoviruses
• Birnaviridae family of dsRNA viruses.

The RNA-directed RNA polymerases in the first of the above superfamilies can be divided into the following three subgroups:

• All positive-strand RNA eukaryotic viruses with no DNA stage
• All RNA-containing bacteriophages -there are two families of RNA-containing bacteriophages: Leviviridae (positive ssRNA phages) and Cystoviridae (dsRNA phages)
• Reoviridae family of dsRNA viruses.

Flaviviruses produce a polyprotein from the ssRNA genome. The polyprotein is cleaved to a number of products, one of which is NS5. Recombinant dengue type 1 virus NS5 protein expressed in Escherichia coli exhibits RNA-dependent RNA polymerase activity. This RNA-directed RNA polymerase possesses a number of short regions and motifs homologous to other RNA-directed RNA polymerases.

See also

• Spiegelman Monster

References

External links

• RNA Replicase at the US National Library of Medicine Medical Subject Headings (MeSH)
• EC 2.7.7.48

This article incorporates text from the public domain Pfam and InterPro IPR000208

UpToDate Contents

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English Journal

• Acute hypoxia affects P-TEFb through HDAC3 and HEXIM1-dependent mechanism to promote gene-specific transcriptional repression.

• Safronova OS1, Nakahama K2, Morita I3.
• Nucleic acids research.Nucleic Acids Res.2014 Oct 1;42(14):8954-69. doi: 10.1093/nar/gku611. Epub 2014 Jul 23.
• Hypoxia is associated with a variety of physiological and pathological conditions and elicits specific transcriptional responses. The elongation competence of RNA Polymerase II is regulated by the positive transcription elongation factor b (P-TEFb)-dependent phosphorylation of Ser2 residues on its C
• PMID 25056306

• Inhibition of RNA binding to hepatitis C virus RNA-dependent RNA polymerase: a new mechanism for antiviral intervention.

• Ahmed-Belkacem A1, Guichou JF2, Brillet R1, Ahnou N1, Hernandez E1, Pallier C3, Pawlotsky JM4.
• Nucleic acids research.Nucleic Acids Res.2014 Oct 1;42(14):9399-409. doi: 10.1093/nar/gku632. Epub 2014 Jul 22.
• The hepatitis C virus (HCV) RNA-dependent RNA polymerase (RdRp) is a key target for antiviral intervention. The goal of this study was to identify the binding site and unravel the molecular mechanism by which natural flavonoids efficiently inhibit HCV RdRp. Screening identified the flavonol querceta
• PMID 25053847

• Spacing requirements for Class I transcription activation in bacteria are set by promoter elements.

• Zhou Y1, Kolb A2, Busby SJ3, Wang YP4.
• Nucleic acids research.Nucleic Acids Res.2014 Oct 1;42(14):9209-16. doi: 10.1093/nar/gku625. Epub 2014 Jul 17.
• The Escherichia coli cAMP receptor protein (CRP) activates transcription initiation at many promoters by binding upstream of core promoter elements and interacting with the C-terminal domain of the RNA polymerase α subunit. Previous studies have shown stringent spacing is required for transcription
• PMID 25034698

Japanese Journal

• An RNA-dependent RNA polymerase gene in bat genomes derived from an ancient negative-strand RNA virus.

• Scientific reports 6, 2016-05-13
• NAID 120005822794

• Truncated yet functional viral protein produced via RNA polymerase slippage implies underestimated coding capacity of RNA viruses

• Scientific reports 6, 2016-02-23
• NAID 120005743057

• Truncated yet functional viral protein produced via RNA polymerase slippage implies underestimated coding capacity of RNA viruses

• Scientific Reports 6, 2016-02-22
• NAID 120005818283

Related Links

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• Structure of the RNA-dependent RNA polymerase of poliovirus

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★リンクテーブル★

リンク元	「RNA依存性RNAポリメラーゼ」
関連記事	「R」「dependent」「RNA」

「RNA依存性RNAポリメラーゼ」

　　[★]

英

RNA-dependent RNA polymerase

関

RNA複製酵素

「R」

　　[★]

• レントゲン roentgen
• アルギニン
• respiratory rate
• respiratory quotient
• プリン
• アルキル基 alkyl group
• 化合物の側鎖

　 　

「dependent」

　　[★]

• adj.

• 依存性の、依存的な、依存型の、依存の

関

depend、dependence、dependency、dependently

　 　 　 　 　

「RNA」

　　[★]

同

リボ核酸 ribonucleic acid RNA

関

DNA

• D-リボースを糖成分とする核酸